Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 410/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ComplexHeatmap 2.21.0  (landing page)
Zuguang Gu
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/ComplexHeatmap
git_branch: devel
git_last_commit: 1e8215b
git_last_commit_date: 2024-04-30 10:42:46 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for ComplexHeatmap on palomino6

To the developers/maintainers of the ComplexHeatmap package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ComplexHeatmap.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ComplexHeatmap
Version: 2.21.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ComplexHeatmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ComplexHeatmap_2.21.0.tar.gz
StartedAt: 2024-07-15 22:55:09 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 23:00:14 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 304.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ComplexHeatmap.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ComplexHeatmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ComplexHeatmap_2.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/ComplexHeatmap.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ComplexHeatmap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ComplexHeatmap' version '2.21.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ComplexHeatmap' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-AnnotationFunction.R'
  Running 'test-ColorMapping-class.R'
  Running 'test-Heatmap-class.R'
  Running 'test-Heatmap-cluster.R'
  Running 'test-HeatmapAnnotation.R'
  Running 'test-HeatmapList-class.R'
  Running 'test-Legend.R'
  Running 'test-SingleAnnotation.R'
  Running 'test-annotation_axis.R'
  Running 'test-dendrogram.R'
  Running 'test-gridtext.R'
  Running 'test-interactive.R'
  Running 'test-multiple-page.R'
  Running 'test-oncoPrint.R'
  Running 'test-pheatmap.R'
  Running 'test-textbox.R'
  Running 'test-upset.R'
  Running 'test-utils.R'
  Running 'testthat-all.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Package vignettes with \VignetteEngine{} not specifying an engine package:
  'complex_heatmap.rmd'
  'most_probably_asked_questions.Rmd'
Engines should be specified as \VignetteEngine{PKG::ENG}.
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/ComplexHeatmap.Rcheck/00check.log'
for details.


Installation output

ComplexHeatmap.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ComplexHeatmap
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'ComplexHeatmap' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ComplexHeatmap)

Tests output

ComplexHeatmap.Rcheck/tests/test-annotation_axis.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> 
> 
> gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 
+     side = "left", facing = "outside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "left", facing = "outside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 
+     side = "left", facing = "inside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "left", facing = "inside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 
+     side = "right", facing = "outside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "right", facing = "outside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 
+     side = "right", facing = "inside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "right", facing = "inside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, 
+     side = "top", facing = "outside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "top", facing = "outside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 90, 
+     side = "top", facing = "outside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "top", facing = "outside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 45, 
+     side = "top", facing = "outside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "top", facing = "outside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, 
+     side = "top", facing = "inside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "top", facing = "inside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, 
+     side = "bottom", facing = "outside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "bottom", facing = "outside"')
> grid.draw(gb)
> popViewport()
> 
> gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, 
+     side = "bottom", facing = "inside")
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> grid.rect()
> grid.text('side = "bottom", facing = "inside"')
> grid.draw(gb)
> popViewport()
> 
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> gb = annotation_axis_grob(labels_rot = 0, side = "left", facing = "outside")
> grid.rect()
> grid.text('side = "left", facing = "outside"')
> grid.draw(gb)
> popViewport()
> 
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> gb = annotation_axis_grob(side = "left", direction = "reverse")
> grid.rect()
> grid.text('side = "left", direction = "reverse')
> grid.draw(gb)
> popViewport()
> 
> grid.newpage()
> pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))
> gb = annotation_axis_grob(side = "bottom", direction = "reverse")
> grid.rect()
> grid.text('side = "bottom", direction = "reverse"')
> grid.draw(gb)
> popViewport()
> 
> 
> 
> proc.time()
   user  system elapsed 
   1.84    0.14    1.95 

ComplexHeatmap.Rcheck/tests/test-AnnotationFunction.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> if(!exists("normalize_graphic_param_to_mat")) {
+ 	normalize_graphic_param_to_mat = ComplexHeatmap:::normalize_graphic_param_to_mat
+ }
> 
> if(!exists("height")) {
+ 	height = ComplexHeatmap:::height
+ }
> 
> if(!exists("width")) {
+ 	width = ComplexHeatmap:::width
+ }
> 
> normalize_graphic_param_to_mat(1, nc = 2, nr = 4, "foo")
     [,1] [,2]
[1,]    1    1
[2,]    1    1
[3,]    1    1
[4,]    1    1
> normalize_graphic_param_to_mat(1:2, nc = 2, nr = 4, "foo")
     [,1] [,2]
[1,]    1    2
[2,]    1    2
[3,]    1    2
[4,]    1    2
> normalize_graphic_param_to_mat(1:4, nc = 2, nr = 4, "foo")
     [,1] [,2]
[1,]    1    1
[2,]    2    2
[3,]    3    3
[4,]    4    4
> 
> ### AnnotationFunction constructor #####
> fun = function(index) {
+ 	x = runif(10)
+ 	pushViewport(viewport(xscale = c(0.5, 10.5), yscale = c(0, 1)))
+ 	grid.points(index, x[index])
+ 	popViewport()
+ }
> anno = AnnotationFunction(fun = fun)
> 
> x = runif(10)
> fun = function(index) {
+ 	pushViewport(viewport(xscale = c(0.5, 10.5), yscale = c(0, 1)))
+ 	grid.points(index, x[index])
+ 	popViewport()
+ }
> anno = AnnotationFunction(fun = fun, var_import = "x")
> anno = AnnotationFunction(fun = fun, var_import = list(x))
> 
> 
> x = runif(10)
> cell_fun = function(i) {
+ 	pushViewport(viewport(yscale = c(0, 1)))
+ 	grid.points(unit(0.5, "npc"), x[i])
+ 	popViewport()
+ }
> anno = AnnotationFunction(cell_fun = cell_fun, var_import = "x")
> ha = HeatmapAnnotation(foo = anno)
> draw(ha, 1:10, test = T)
> 
> cell_fun = function(i) {
+ 	pushViewport(viewport(xscale = c(0, 1)))
+ 	grid.points(x[i], unit(0.5, "npc"))
+ 	popViewport()
+ }
> anno = AnnotationFunction(cell_fun = cell_fun, var_import = "x", which = "row")
> ha = rowAnnotation(foo = anno)
> draw(ha, 1:10, test = T)
> 
> # devAskNewPage(ask = dev.interactive())
> 
> ########### testing anno_simple ############
> anno = anno_simple(1:10)
> draw(anno, test = "as a simple vector")
> draw(anno[1:5], test = "subset of column annotation")
> anno = anno_simple(1:10, which = "row")
> draw(anno, test = "as row annotation")
> draw(anno[1:5], test = "subste of row annotation")
> 
> anno = anno_simple(1:10, col = structure(rand_color(10), names = 1:10))
> draw(anno, test = "self-define colors")
> 
> anno = anno_simple(1:10, border = TRUE)
> draw(anno, test = "border")
> anno = anno_simple(1:10, gp = gpar(col = "red"))
> draw(anno, test = "gp for the grids")
> 
> anno = anno_simple(c(1:9, NA))
> draw(anno, test = "vector has NA values")
> 
> anno = anno_simple(cbind(1:10, 10:1))
> draw(anno, test = "a matrix")
> draw(anno[1:5], test = "subste of a matrix")
> 
> anno = anno_simple(1:10, pch = 1, pt_gp = gpar(col = "red"), pt_size = unit(seq(1, 10), "mm"))
> draw(anno, test = "with symbols + pt_gp + pt_size")
> anno = anno_simple(1:10, pch = 1:10)
> draw(anno, test = "pch is a vector")
> anno = anno_simple(1:10, pch = c(1:4, NA, 6:8, NA, 10, 11))
> draw(anno, test = "pch has NA values")
> 
> anno = anno_simple(cbind(1:10, 10:1), pch = 1, pt_gp = gpar(col = "blue"))
> draw(anno, test = "matrix with symbols")
> anno = anno_simple(cbind(1:10, 10:1), pch = 1:2)
> draw(anno, test = "matrix, length of pch is number of annotations")
> anno = anno_simple(cbind(1:10, 10:1), pch = 1:10)
> draw(anno, test = "matrix, length of pch is length of samples")
> anno = anno_simple(cbind(1:10, 10:1), pch = matrix(1:20, nc = 2))
> draw(anno, test = "matrix, pch is a matrix")
> pch = matrix(1:20, nc = 2)
> pch[sample(length(pch), 10)] = NA
> anno = anno_simple(cbind(1:10, 10:1), pch = pch)
> draw(anno, test = "matrix, pch is a matrix with NA values")
> 
> 
> ####### test anno_empty ######
> anno = anno_empty()
> draw(anno, test = "anno_empty")
> anno = anno_empty(border = FALSE)
> draw(anno, test = "anno_empty without border")
> 
> if(0) {
+ ###### test anno_image #####
+ image1 = sample(dir("~/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10)
+ anno = anno_image(image1)
+ draw(anno, test = "png")
+ draw(anno[1:5], test = "subset of png")
+ anno = anno_image(image1, which = "row")
+ draw(anno, test = "png on rows")
+ image2 = sample(dir("~/Downloads/IcoMoon-Free-master/SVG/", full.names = TRUE), 10)
+ anno = anno_image(image2)
+ draw(anno, test = "svg")
+ image3 = sample(dir("~/Downloads/IcoMoon-Free-master/EPS/", full.names = TRUE), 10)
+ anno = anno_image(image3)
+ draw(anno, test = "eps")
+ image4 = sample(dir("~/Downloads/IcoMoon-Free-master/PDF/", full.names = TRUE), 10)
+ anno = anno_image(image4)
+ draw(anno, test = "pdf")
+ 
+ anno = anno_image(c(image1[1:3], image2[1:3], image3[1:3], image4[1:3]))
+ draw(anno, test = "png+svg+eps+pdf")
+ 
+ anno = anno_image(image1, gp = gpar(fill = 1:10, col = "black"))
+ draw(anno, test = "png + gp")
+ draw(anno[1:5], test = "png + gp")
+ 
+ anno = anno_image(image1, space = unit(3, "mm"))
+ draw(anno, test = "space")
+ 
+ image1[1] = ""
+ anno = anno_image(image1)
+ draw(anno, test = "png")
+ }
> 
> ######## test anno_points #####
> anno = anno_points(runif(10))
> draw(anno, test = "anno_points")
> anno = anno_points(matrix(runif(20), nc = 2), pch = 1:2)
> draw(anno, test = "matrix")
> anno = anno_points(c(1:5, 1:5))
> draw(anno, test = "anno_points")
> anno = anno_points(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3))
> draw(anno, test = "matrix")
> 
> anno = anno_points(1:10, gp = gpar(col = rep(2:3, each = 5)), pch = rep(2:3, each = 5))
> draw(anno, test = "anno_points")
> draw(anno, index = c(1, 3, 5, 7, 9, 2, 4, 6, 8, 10), test = "anno_points")
> 
> anno = anno_points(c(1:5, NA, 7:10))
> draw(anno, test = "anno_points")
> 
> 
> anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1))
> draw(anno, test = "anno_points")
> 
> anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1), which = "row")
> draw(anno, test = "anno_points")
> 
> # pch as image
> if(0) {
+ image1 = sample(dir("/desktop-home/guz/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10)
+ x = runif(10)
+ anno1 = anno_points(x, pch = image1, pch_as_image = TRUE, size = unit(5, "mm"), height = unit(4, "cm"))
+ anno2 = anno_points(x, height = unit(4, "cm"))
+ draw(anno1, test = "anno_points")
+ draw(anno2, test = "anno_points")
+ }
> 
> ##### test anno_lines ###
> anno = anno_lines(runif(10))
> draw(anno, test = "anno_lines")
> anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3))
> draw(anno, test = "matrix")
> anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3),
+ 	add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16))
> draw(anno, test = "matrix")
> anno = anno_lines(sort(rnorm(10)), height = unit(2, "cm"), smooth = TRUE, add_points = TRUE)
> draw(anno, test = "anno_lines, smooth")
> anno = anno_lines(cbind(sort(rnorm(10)), sort(rnorm(10), decreasing = TRUE)), 
+ 	height = unit(2, "cm"), smooth = TRUE, add_points = TRUE, gp = gpar(col = 2:3))
> draw(anno, test = "anno_lines, smooth, matrix")
> 
> anno = anno_lines(sort(rnorm(10)), width = unit(2, "cm"), smooth = TRUE, add_points = TRUE, which = "row")
> draw(anno, test = "anno_lines, smooth, by row")
> anno = anno_lines(cbind(sort(rnorm(10)), sort(rnorm(10), decreasing = TRUE)), 
+ 	width = unit(2, "cm"), smooth = TRUE, add_points = TRUE, gp = gpar(col = 2:3), which = "row")
> draw(anno, test = "anno_lines, smooth, matrix, by row")
> 
> anno = anno_lines(c(1:5, NA, 7:10))
> draw(anno, test = "anno_lines")
> 
> anno = anno_lines(runif(10), axis_param = list(direction = "reverse"))
> draw(anno, test = "anno_lines")
> 
> ###### test anno_text #######
> anno = anno_text(month.name)
> draw(anno, test = "month names")
> anno = anno_text(month.name, gp = gpar(fontsize = 16))
> draw(anno, test = "month names with fontsize")
> anno = anno_text(month.name, gp = gpar(fontsize = 1:12+4))
> draw(anno, test = "month names with changing fontsize")
> anno = anno_text(month.name, which = "row")
> draw(anno, test = "month names on rows")
> anno = anno_text(month.name, location = 0, rot = 45, just = "left", gp = gpar(col = 1:12))
> draw(anno, test = "with rotations")
> anno = anno_text(month.name, location = 1, rot = 45, just = "right", gp = gpar(fontsize = 1:12+4))
> draw(anno, test = "with rotations")
> 
> 
> for(rot in seq(0, 360, by = 45)) {
+ 	anno = anno_text(month.name, which = "row", location = 0, rot = rot, 
+ 		just = "left")
+ 	draw(anno, test = paste0("rot =", rot))
+ }
> 
> 
> ##### test anno_barplot #####
> anno = anno_barplot(1:10)
> draw(anno, test = "a vector")
> draw(anno[1:5], test = "a vector, subset")
> anno = anno_barplot(1:10, which = "row")
> draw(anno, test = "a vector")
> anno = anno_barplot(1:10, bar_width = 1)
> draw(anno, test = "bar_width")
> anno = anno_barplot(1:10, gp = gpar(fill = 1:10))
> draw(anno, test = "fill colors")
> 
> anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)))
> draw(anno, test = "a matrix")
> draw(anno[1:5], test = "a matrix, subset")
> anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), which = "row")
> draw(anno, test = "a matrix, on rows")
> anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), gp = gpar(fill = 2:3, col = 2:3))
> draw(anno, test = "a matrix with fill")
> 
> m = matrix(runif(4*10), nc = 4)
> m = t(apply(m, 1, function(x) x/sum(x)))
> anno = anno_barplot(m)
> draw(anno, test = "proportion matrix")
> anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm"))
> draw(anno, test = "proportion matrix")
> 
> anno = anno_barplot(c(1:5, NA, 7:10))
> draw(anno, test = "a vector")
> 
> anno = anno_barplot(1:10, which = "row", axis_param = list(direction = "reverse"))
> draw(anno, test = "a vector")
> 
> anno = anno_barplot(1:10, baseline = 5, which = "row", axis_param = list(direction = "reverse"))
> draw(anno, test = "a vector")
> 
> anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), which = "row", axis_param = list(direction = "reverse"))
> draw(anno, test = "a vector")
> 
> 
> anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), beside = TRUE)
> draw(anno, test = "a matrix")
> draw(anno[1:5], test = "a matrix, subset")
> anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), beside = TRUE, which = "row")
> draw(anno, test = "a matrix, on rows")
> anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), beside = TRUE, gp = gpar(fill = 2:3, col = 2:3))
> draw(anno, test = "a matrix with fill")
> 
> 
> ##### test anno_boxplot #####
> set.seed(123)
> m = matrix(rnorm(100), 10)
> anno = anno_boxplot(m, height = unit(4, "cm"))
> draw(anno, test = "anno_boxplot")
> draw(anno[1:5], test = "subset")
> anno = anno_boxplot(m, height = unit(4, "cm"), gp = gpar(fill = 1:10))
> draw(anno, test = "anno_boxplot with gp")
> anno = anno_boxplot(m, height = unit(4, "cm"), box_width = 0.9)
> draw(anno, test = "anno_boxplot with box_width")
> 
> m = matrix(rnorm(100), 10)
> m[1, ] = NA
> anno = anno_boxplot(m, height = unit(4, "cm"))
> draw(anno, test = "anno_boxplot")
> 
> 
> ####### test anno_joyplot ####
> m = matrix(rnorm(1000), nc = 10)
> lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
> anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row")
> draw(anno, test = "joyplot")
> anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = 1:10))
> draw(anno, test = "joyplot + col")
> anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", scale = 1)
> draw(anno, test = "joyplot + scale")
> 
> m = matrix(rnorm(5000), nc = 50)
> lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
> anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = NA), scale = 4)
> draw(anno, test = "joyplot")
> 
> ######## test anno_horizon ######
> lt = lapply(1:20, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
> anno = anno_horizon(lt, which = "row")
> draw(anno, test = "horizon chart")
> anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = "orange", neg_fill = "darkgreen"))
> draw(anno, test = "horizon chart, col")
> anno = anno_horizon(lt, which = "row", negative_from_top = TRUE)
> draw(anno, test = "horizon chart + negative_from_top")
> anno = anno_horizon(lt, which = "row", gap = unit(1, "mm"))
> draw(anno, test = "horizon chart + gap")
> anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = rep(c("orange", "red"), each = 10),
+ 	neg_fill = rep(c("darkgreen", "blue"), each = 10)))
> draw(anno, test = "horizon chart, col")
> 
> ####### test anno_histogram ####
> m = matrix(rnorm(1000), nc = 10)
> anno = anno_histogram(t(m), which = "row")
> draw(anno, test = "row histogram")
> draw(anno[1:5], test = "subset row histogram")
> anno = anno_histogram(t(m), which = "row", gp = gpar(fill = 1:10))
> draw(anno, test = "row histogram with color")
> anno = anno_histogram(t(m), which = "row", n_breaks = 20)
> draw(anno, test = "row histogram with color")
> m[1, ] = NA
> anno = anno_histogram(t(m), which = "row")
> draw(anno, test = "row histogram")
> 
> 
> ####### test anno_density ######
> anno = anno_density(t(m), which = "row")
> draw(anno, test = "normal density")
> draw(anno[1:5], test = "normal density, subset")
> anno = anno_density(t(m), which = "row", type = "violin")
> draw(anno, test = "violin")
> anno = anno_density(t(m), which = "row", type = "heatmap")
> draw(anno, test = "heatmap")
> anno = anno_density(t(m), which = "row", type = "heatmap", heatmap_colors = c("white", "orange"))
> draw(anno, test = "heatmap, colors")
> 
> anno = anno_density(t(m), which = "row", xlim = c(-2, 2))
> draw(anno, test = "normal density")
> anno = anno_density(t(m), which = "row", type = "violin", xlim = c(-2, 2))
> draw(anno, test = "violin")
> anno = anno_density(t(m), which = "row", type = "heatmap", xlim = c(-2, 2))
> draw(anno, test = "heatmap")
> 
> ###### anno_mark ###
> if(0) {
+ library(gridtext)
+ grid.text = function(text, x = 0.5, y = 0.5, gp = gpar(), rot = 0, default.units = "npc", just = "center") {
+ 	if(length(just) == 1) {
+ 		if(just == "center") {
+ 			just = c("center", "center")
+ 		} else if(just == "bottom") {
+ 			just = c("center", "bottom")
+ 		} else if (just == "top") {
+ 			just = c("center", "top")
+ 		} else if(just == "left") {
+ 			just = c("left", "center")
+ 		} else if(just == "right") {
+ 			just = c("right", "center")
+ 		}
+ 	}
+ 	just2 = c(0.5, 0.5)
+ 	if(is.character(just)) {
+ 		just2[1] = switch(just[1], "center" = 0.5, "left" = 0, "right" = 1)
+ 		just2[2] = switch(just[2], "center" = 0.5, "bottom" = 0, "top" = 1)
+ 	}
+ 	gb = richtext_grob(text, x = x, y = y, gp = gpar(fontsize = 10), box_gp = gpar(col = "black"),
+ 		default.units = default.units, hjust = just2[1], vjust = just2[2], rot = rot)
+ 	grid.draw(gb)
+ }
+ }
> anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
> draw(anno, index = 1:100, test = "anno_mark")
> 
> anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], labels_rot = 30, which = "column")
> draw(anno, index = 1:100, test = "anno_mark")
> 
> m = matrix(1:1000, byrow = TRUE, nr = 100)
> anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row", labels_rot = 30)
> Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
> Heatmap(m) + rowAnnotation(mark = anno)
> 
> ht_list = Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
> draw(ht_list, row_split = c(rep("a", 95), rep("b", 5)))
> 
> 
> grid.newpage()
> pushViewport(viewport(x = 0.45, w = 0.7, h = 0.95))
> h = unit(0, "mm")
> for(rot in seq(0, 360, by = 30)[-13]) {
+ 	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "column", side = "bottom")
+ 	h = h + height(anno)
+ 	pushViewport(viewport(y = h, height = height(anno), just = "top"))
+ 	grid.rect()
+ 	draw(anno, index = 1:100)
+ 	grid::grid.text(qq("labels_rot = @{rot}"), unit(1, "npc") + unit(2, "mm"), just = "left")
+ 	popViewport()
+ }
> 
> 
> grid.newpage()
> pushViewport(viewport(w = 0.9, h = 0.9))
> w = unit(0, "mm")
> for(rot in seq(0, 360, by = 30)) {
+ 	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "row", side = "left")
+ 	w = w + width(anno)
+ 	pushViewport(viewport(x = w, width = width(anno), just = "right"))
+ 	grid.rect()
+ 	draw(anno, index = 1:100)
+ 	popViewport()
+ }
> 
> 
> 
> ### graphic parameters after reordering
> index = c(1, 3, 5, 7, 9, 2, 4, 6, 8, 10)
> anno = anno_simple(1:10, pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
+ 	pt_size = unit(1:10, "mm"))
> draw(anno, index, test = "a numeric vector")
> anno = anno_simple(1:10, pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
+ 	pt_size = unit(1:10, "mm"), which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> 
> anno = anno_points(1:10, pch = 1:10, gp = gpar(col = rep(c(1, 2), each = 5)),
+ 	size = unit(1:10, "mm"))
> draw(anno, index, test = "a numeric vector")
> anno = anno_points(1:10, pch = 1:10, gp = gpar(col = rep(c(1, 2), each = 5)),
+ 	size = unit(1:10, "mm"), which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> 
> anno = anno_lines(sort(runif(10)), pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
+ 	size = unit(1:10, "mm"), add_points = TRUE)
> draw(anno, index, test = "a numeric vector")
> anno = anno_lines(sort(runif(10)), pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
+ 	size = unit(1:10, "mm"), add_points = TRUE, which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> 
> anno = anno_barplot(1:10, gp = gpar(fill = rep(c(1, 2), each = 5)))
> draw(anno, index, test = "a numeric vector")
> anno = anno_barplot(1:10, gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> anno = anno_barplot(cbind(1:10, 10:1), gp = gpar(fill = 1:2))
> draw(anno, index, test = "a numeric vector")
> anno = anno_barplot(cbind(1:10, 10:1), gp = gpar(fill = 1:2), which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> 
> m = matrix(rnorm(100), 10)
> m = m[, order(apply(m, 2, median))]
> anno = anno_boxplot(m, pch = 1:10, gp = gpar(fill = rep(c(1, 2), each = 5)),
+ 	size = unit(1:10, "mm"), height = unit(4, "cm"))
> draw(anno, index, test = "a numeric vector")
> anno = anno_boxplot(t(m), pch = 1:10, gp = gpar(fill = rep(c(1, 2), each = 5)),
+ 	size = unit(1:10, "mm"), which = "row", width = unit(4, "cm"))
> draw(anno, index, test = "a numeric vector")
> 
> anno = anno_histogram(m, gp = gpar(fill = rep(c(1, 2), each = 5)))
> draw(anno, index, test = "a numeric vector")
> anno = anno_histogram(t(m), gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> anno = anno_density(m, gp = gpar(fill = rep(c(1, 2), each = 5)))
> draw(anno, index, test = "a numeric vector")
> anno = anno_density(t(m), gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> 
> anno = anno_density(m, type = "violin", gp = gpar(fill = rep(c(1, 2), each = 5)))
> draw(anno, index, test = "a numeric vector")
> anno = anno_density(t(m), type = "violin", gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> 
> anno = anno_text(month.name, gp = gpar(col = rep(c(1, 2), each = 5)))
> draw(anno, index, test = "a numeric vector")
> anno = anno_text(month.name, gp = gpar(col = rep(c(1, 2), each = 5)), which= "row")
> draw(anno, index, test = "a numeric vector")
> 
> lt = lapply(1:10, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
> anno = anno_horizon(lt, gp = gpar(pos_fill = rep(c(1, 2), each = 5), neg_fill = rep(c(3, 4), each = 5)), which = "row")
> draw(anno, index, test = "a numeric vector")
> 
> m = matrix(rnorm(1000), nc = 10)
> lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
> anno = anno_joyplot(lt, gp = gpar(fill = rep(c(1, 2), each = 5)), 
+ 	width = unit(4, "cm"), which = "row")
> draw(anno, index, test = "joyplot")
> 
> 
> anno = anno_block(gp = gpar(fill = 1:4))
> draw(anno, index = 1:10, k = 1, n = 4, test = "anno_block")
> draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
> 
> anno = anno_block(gp = gpar(fill = 1:4), labels = letters[1:4], labels_gp = gpar(col = "white"))
> draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
> draw(anno, index = 1:10, k = 4, n = 4, test = "anno_block")
> # draw(anno, index = 1:10, k = 2, n = 2, test = "anno_block")
> 
> anno = anno_block(gp = gpar(fill = 1:4), labels = letters[1:4], labels_gp = gpar(col = "white"), which = "row")
> draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
> 
> 
> ### anno_zoom
> fa = sort(sample(letters[1:3], 100, replace = TRUE, prob = c(1, 2, 3)))
> panel_fun = function(index, nm) {
+ 	grid.rect()
+ 	grid.text(nm)
+ }
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun)
> draw(anno, index = 1:100, test = "anno_zoom")
> 
> anno = anno_zoom(align_to = list(a = which(fa == "a")), which = "row", panel_fun = panel_fun)
> draw(anno, index = 1:100, test = "anno_zoom")
> 
> 
> panel_fun = function(index, nm) {
+ 	grid.rect(gp = gpar(fill = "grey", col = NA))
+ 	grid.text(nm)
+ }
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun, link_gp = gpar(fill = "grey", col = "black"), internal_line = FALSE)
> draw(anno, index = 1:100, test = "anno_zoom")
> 
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	gap = unit(1, "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, set gap")
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = 1:3)
> draw(anno, index = 1:100, test = "anno_zoom, size set as relative values")
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = 1:3, extend = unit(1, "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, extend")
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = unit(1:3, "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, size set as absolute values")
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = unit(c(2, 20, 40), "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, big size")
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = 1:3, gap = unit(1, "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, size set as relative values, gap")
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = unit(1:3, "cm"), gap = unit(1, "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, size set as absolute values, gap")
> 
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = unit(1:3, "cm"), side = "left")
> draw(anno, index = 1:100, test = "anno_zoom, side")
> 
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = unit(1:3, "cm"), link_gp = gpar(fill = 1:3))
> draw(anno, index = 1:100, test = "anno_zoom, link_gp")
> 
> anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
+ 	size = unit(1:3, "cm"), link_gp = gpar(fill = 1:3),
+ 	link_width = unit(2, "cm"), width = unit(4, "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, width")
> 
> anno = anno_zoom(align_to = list(a = 1:10, b = 30:45, c = 70:90), 
+ 	which = "row", panel_fun = panel_fun, size = unit(1:3, "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, a list of indices")
> 
> anno = anno_zoom(align_to = fa, which = "column", panel_fun = panel_fun,
+ 	size = unit(1:3, "cm"))
> draw(anno, index = 1:100, test = "anno_zoom, column annotation")
> 
> 
> m = matrix(rnorm(100*10), nrow = 100)
> hc = hclust(dist(m))
> fa2 = cutree(hc, k = 4)
> anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun)
> draw(anno, index = hc$order, test = "anno_zoom, column annotation")
> 
> anno = anno_zoom(align_to = fa2, which = "column", panel_fun = panel_fun)
> draw(anno, index = hc$order, test = "anno_zoom, column annotation")
> 
> 
> anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun)
> draw(Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno)))
> draw(Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno), row_split = 2))
> 
> 
> anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun, size = unit(1:4, "cm"))
> draw(Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno)))
> 
> set.seed(123)
> m = matrix(rnorm(100*10), nrow = 100)
> subgroup = sample(letters[1:3], 100, replace = TRUE, prob = c(1, 5, 10))
> rg = range(m)
> panel_fun = function(index, nm) {
+ 	pushViewport(viewport(xscale = rg, yscale = c(0, 2)))
+ 	grid.rect()
+ 	grid.xaxis(gp = gpar(fontsize = 8))
+ 	grid.boxplot(m[index, ], pos = 1, direction = "horizontal")
+ 	grid.text(paste("distribution of group", nm), mean(rg), y = 1.9, 
+ 		just = "top", default.units = "native", gp = gpar(fontsize = 10))
+ 	popViewport()
+ }
> anno = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun, 
+ 	size = unit(2, "cm"), gap = unit(1, "cm"), width = unit(4, "cm"))
> draw(Heatmap(m, right_annotation = rowAnnotation(foo = anno), row_split = subgroup))
> 
> panel_fun2 = function(index, nm) {
+ 	pushViewport(viewport())
+ 	grid.rect()
+ 	n = floor(length(index)/4)
+ 	txt = paste("gene function", 1:n, collapse = "\n")
+ 	grid.text(txt, 0.95, 0.5, default.units = "npc", just = "right", gp = gpar(fontsize = 8))
+ 	popViewport()
+ }
> anno2 = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun2, 
+ 	gap = unit(1, "cm"), width = unit(3, "cm"), side = "left")
> 
> draw(Heatmap(m, right_annotation = rowAnnotation(subgroup = subgroup, foo = anno,
+ 	show_annotation_name = FALSE), 
+ 	left_annotation = rowAnnotation(bar = anno2, subgroup = subgroup, show_annotation_name = FALSE),
+ 	show_row_dend = FALSE,
+ 	row_split = subgroup))
> 
> draw(Heatmap(m, right_annotation = rowAnnotation(foo = anno), 
+ 	left_annotation = rowAnnotation(bar = anno2),
+ 	show_row_dend = FALSE,
+ 	row_split = subgroup))
> 
> set.seed(12345)
> mat = matrix(rnorm(30*10), nr = 30)
> row_split = c(rep("a", 10), rep("b", 5), rep("c", 2), rep("d", 3), 
+ 	          rep("e", 2), letters[10:17])
> row_split = factor(row_split)
> 
> panel_fun = function(index, name) {
+ 	pushViewport(viewport())
+ 	grid.rect()
+ 	grid.text(name)
+ 	popViewport()
+ }
> 
> anno = anno_zoom(align_to = row_split, which = "row", panel_fun = panel_fun, 
+ 	size = unit(0.5, "cm"), width = unit(4, "cm"))
> 
> # > dev.size()
> # [1] 3.938326 4.502203
> dev.new(width = 3.938326, height = 4.502203)
dev.new(): using pdf(file="Rplots1.pdf")
> draw(Heatmap(mat, right_annotation = rowAnnotation(foo = anno), 
+ 	row_split = row_split))
> 
> 
> 
> #### anno_customize ###
> x = sort(sample(letters[1:3], 10, replace = TRUE))
> graphics = list(
+ 	"a" = function(x, y, w, h) grid.points(x, y, pch = 16),
+ 	"b" = function(x, y, w, h) grid.rect(x, y, w*0.8, h*0.8, gp = gpar(fill = "red")),
+ 	"c" = function(x, y, w, h) grid.segments(x - 0.5*w, y - 0.5*h, x + 0.5*w, y + 0.5*h, gp = gpar(lty = 2))
+ )
> 
> anno = anno_customize(x, graphics = graphics)
> draw(anno, index = 1:10, test = "")
> 
> anno = anno_customize(c(x, "d"), graphics = graphics)
Note: following levels in `x` have no graphics defined:
    d.
Set `verbose = FALSE` in `anno_customize()` to turn off this message.
> 
> ### anno_numeric ##
> x = runif(10)
> anno = anno_numeric(x)
> draw(anno, 1:10, test = TRUE)
> anno = anno_numeric(x, align_to = "right")
> draw(anno, 1:10, test = TRUE)
> 
> 
> x = 10^(-runif(10, 1, 6))
> anno = anno_numeric(x, x_convert = function(x) -log10(x), labels_format = function(x) sprintf("%.2e", x))
> draw(anno, 1:10, test = TRUE)
> 
> x = runif(10, -1, 1)
> anno = anno_numeric(x)
> draw(anno, 1:10, test = TRUE)
> anno = anno_numeric(x, labels_gp = gpar(col = c("green", "red")))
> draw(anno, 1:10, test = TRUE)
> 
> anno = anno_numeric(x, bg_gp = gpar(col = c("green", "red")))
> draw(anno, 1:10, test = TRUE)
> 
> 
> x = runif(10, 0.5, 1.5)
> anno = anno_numeric(x, align_to = 0)
> draw(anno, 1:10, test = TRUE)
> 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  15.25    1.07   15.89 

ComplexHeatmap.Rcheck/tests/test-ColorMapping-class.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> cm = ColorMapping(name = "test",
+ 	colors = c("blue", "white", "red"),
+ 	levels = c("a", "b", "c"))
> color_mapping_legend(cm)
> 
> cm = ColorMapping(name = "test",
+ 	col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")))
> color_mapping_legend(cm)
> 
> cm = ColorMapping(name = "test",
+ 	colors = c("blue", "white", "red"),
+ 	levels = c(1, 2, 3))
> color_mapping_legend(cm)
> 
> ha = SingleAnnotation(value = rep(NA, 10), name = "foo")
> cm = ha@color_mapping
> color_mapping_legend(cm)
> 
> 
> proc.time()
   user  system elapsed 
   1.90    0.21    2.12 

ComplexHeatmap.Rcheck/tests/test-dendrogram.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> if(!exists("cut_dendrogram")) {
+ 	cut_dendrogram = ComplexHeatmap:::cut_dendrogram
+ }
> 
> library(dendextend)

---------------------
Welcome to dendextend version 1.17.1
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
You may ask questions at stackoverflow, use the r and dendextend tags: 
	 https://stackoverflow.com/questions/tagged/dendextend

	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
---------------------


Attaching package: 'dendextend'

The following object is masked from 'package:stats':

    cutree

> 
> m = matrix(rnorm(100), 10)
> dend1 = as.dendrogram(hclust(dist(m)))
> dend1 = adjust_dend_by_x(dend1, sort(runif(10)))
> 
> m = matrix(rnorm(50), nr = 5)
> dend2 = as.dendrogram(hclust(dist(m)))
> 
> dend3 = as.dendrogram(hclust(dist(m[1:2, ])))
> 
> 
> dend_merge = merge_dendrogram(dend3, 
+ 	list(set(dend1, "branches_col", "red"), 
+ 		 set(dend2, "branches_col", "blue"))
+ )
> 
> grid.dendrogram(dend_merge, test = TRUE, facing = "bottom")
> grid.dendrogram(dend_merge, test = TRUE, facing = "top")
> grid.dendrogram(dend_merge, test = TRUE, facing = "left")
> grid.dendrogram(dend_merge, test = TRUE, facing = "right")
> 
> grid.dendrogram(dend_merge, test = TRUE, facing = "bottom", order = "reverse")
> grid.dendrogram(dend_merge, test = TRUE, facing = "top", order = "reverse")
> grid.dendrogram(dend_merge, test = TRUE, facing = "left", order = "reverse")
> grid.dendrogram(dend_merge, test = TRUE, facing = "right", order = "reverse")
> 
> 
> m = matrix(rnorm(100), 10)
> dend1 = as.dendrogram(hclust(dist(m)))
> dend1 = adjust_dend_by_x(dend1, unit(1:10, "cm"))
> grid.dendrogram(dend1, test = TRUE)
> 
> dl = cut_dendrogram(dend1, k = 3)
> grid.dendrogram(dl$upper, test = TRUE)
> 
> 
> m1 = matrix(rnorm(100), nr = 10)
> m2 = matrix(rnorm(80), nr = 8)
> m3 = matrix(rnorm(50), nr = 5)
> dend1 = as.dendrogram(hclust(dist(m1)))
> dend2 = as.dendrogram(hclust(dist(m2)))
> dend3 = as.dendrogram(hclust(dist(m3)))
> dend_p = as.dendrogram(hclust(dist(rbind(colMeans(m1), colMeans(m2), colMeans(m3)))))
> dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3))
> grid.dendrogram(dend_m, test = T)
> 
> dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3), only_parent = TRUE)
> grid.dendrogram(dend_m, test = T)
> 
> require(dendextend)
> dend1 = color_branches(dend1, k = 1, col = "red")
> dend2 = color_branches(dend2, k = 1, col = "blue")
> dend3 = color_branches(dend3, k = 1, col = "green")
> dend_p = color_branches(dend_p, k = 1, col = "orange")
> dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3))
> grid.dendrogram(dend_m, test = T)
> 
> 
> m = matrix(rnorm(120), nc = 12)
> colnames(m) = letters[1:12]
> fa = rep(c("a", "b", "c"), times = c(2, 4, 6))
> dend = cluster_within_group(m, fa)
> grid.dendrogram(dend, test = TRUE)
> 
> 
> # stack overflow problem
> m = matrix(1, nrow = 1000, ncol = 10)
> m[1, 2] = 2
> dend = as.dendrogram(hclust(dist(m)))
> grid.dendrogram(dend, test = T)
> 
> # node attr
> m = matrix(rnorm(100), 10)
> dend = as.dendrogram(hclust(dist(m)))
> require(dendextend)
> dend1 = color_branches(dend, k = 2, col = 1:2)
> grid.dendrogram(dend1, test = T)
> dend1 = dend
> dend1 = dendrapply(dend, function(d) {
+ 	attr(d, "nodePar") = list(pch = sample(20, 1), cex = runif(1, min = 0.3, max = 1.3), col = rand_color(1))
+ 	d
+ })
> grid.dendrogram(dend1, test = T)
> 
> Heatmap(m, cluster_rows = dend1, cluster_columns = dend1)
> 
> d1 = ComplexHeatmap:::dend_edit_node(dend, method = "top-bottom", function(d, index) {
+ 	attr(d, "depth") = length(index)
+ 	d
+ })
> 
> d2 = ComplexHeatmap:::dend_edit_node(dend, method = "bottom-top", function(d, index) {
+ 	attr(d, "depth") = length(index)
+ 	d
+ })
> 
> identical(d1, d2)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   5.57    0.65    5.90 

ComplexHeatmap.Rcheck/tests/test-gridtext.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> 
> if(requireNamespace("gridtext")) {
+ ##### test anno_richtext ####
+ mat = matrix(rnorm(100), 10)
+ rownames(mat) = letters[1:10]
+ ht = Heatmap(mat, 
+ 	column_title = gt_render("Some <span style='color:blue'>blue text **in bold.**</span><br>And *italics text.*<br>And some <span style='font-size:18pt; color:black'>large</span> text.", r = unit(2, "pt"), padding = unit(c(2, 2, 2, 2), "pt")),
+ 	column_title_gp = gpar(box_fill = "orange"),
+ 	row_labels = gt_render(letters[1:10], padding = unit(c(2, 10, 2, 10), "pt")),
+ 	row_names_gp = gpar(box_col = rep(2:3, times = 5), box_fill = ifelse(1:10%%2, "yellow", "white")),
+ 	row_km = 2, 
+ 	row_title = gt_render(c("title1", "title2")), 
+ 	row_title_gp = gpar(box_fill = "yellow"),
+ 	heatmap_legend_param = list(
+ 		title = gt_render("<span style='color:orange'>**Legend title**</span>"), 
+ 		title_gp = gpar(box_fill = "grey"),
+ 		at = c(-3, 0, 3), 
+ 		labels = gt_render(c("*negative* three", "zero", "*positive* three"))
+ 	))
+ ht = rowAnnotation(
+ 	foo = anno_text(gt_render(sapply(LETTERS[1:10], strrep, 10), align_widths = TRUE), 
+ 	                gp = gpar(box_col = "blue", box_lwd = 2), 
+ 	                just = "right", 
+ 	                location = unit(1, "npc")
+ 	)) + ht
+ draw(ht)
+ 
+ }
Loading required namespace: gridtext
> 
> proc.time()
   user  system elapsed 
   3.92    0.65    4.10 

ComplexHeatmap.Rcheck/tests/test-Heatmap-class.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> set.seed(123)
> nr1 = 10; nr2 = 8; nr3 = 6
> nc1 = 6; nc2 = 8; nc3 = 10
> mat = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1,   sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc1, mean = 0,   sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc1, mean = 0,   sd = 0.5), nr = nr3)),
+     rbind(matrix(rnorm(nr1*nc2, mean = 0,   sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc2, mean = 1,   sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc2, mean = 0,   sd = 0.5), nr = nr3)),
+     rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc3, mean = 1,   sd = 0.5), nr = nr3))
+    )
> 
> rownames(mat) = paste0("row", seq_len(nrow(mat)))
> colnames(mat) = paste0("column", seq_len(nrow(mat)))
> 
> ht = Heatmap(mat)
> draw(ht, test = TRUE)
> ht
> 
> 
> ht = Heatmap(mat, col = colorRamp2(c(-3, 0, 3), c("green", "white", "red")))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, name = "test")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, rect_gp = gpar(col = "black"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, border = "red")
> draw(ht, test = TRUE)
> 
> ######## test title ##########
> ht = Heatmap(mat, row_title = "blablabla")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_title = "blablabla", row_title_side = "right")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_title = "blablabla", row_title_gp = gpar(fontsize = 20, font = 2))
> draw(ht, test = TRUE)
> 
> # ht = Heatmap(mat, row_title = "blablabla", row_title_rot = 45)
> # draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_title = "blablabla", row_title_rot = 0)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_title = "blablabla", row_title_gp = gpar(fill = "red", col = "white"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_title = "blablabla")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_title = "blablabla", column_title_side = "bottom")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_title = "blablabla", column_title_gp = gpar(fontsize = 20, font = 2))
> draw(ht, test = TRUE)
> 
> # ht = Heatmap(mat, column_title = "blablabla", column_title_rot = 45)
> # draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_title = "blablabla", column_title_rot = 90)
> draw(ht, test = TRUE)
> 
> 
> ### test clustering ####
> 
> ht = Heatmap(mat, cluster_rows = FALSE)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, clustering_distance_rows = "pearson")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, clustering_distance_rows = function(x) dist(x))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, clustering_distance_rows = function(x, y) 1 - cor(x, y))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, clustering_method_rows = "single")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_dend_side = "right")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_dend_width = unit(4, "cm"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_dend_gp = gpar(lwd = 2, col = "red"))
> draw(ht, test = TRUE)
> 
> dend = as.dendrogram(hclust(dist(mat)))
> ht = Heatmap(mat, cluster_rows = dend)
> draw(ht, test = TRUE)
> 
> library(dendextend)

---------------------
Welcome to dendextend version 1.17.1
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
You may ask questions at stackoverflow, use the r and dendextend tags: 
	 https://stackoverflow.com/questions/tagged/dendextend

	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
---------------------


Attaching package: 'dendextend'

The following object is masked from 'package:stats':

    cutree

> dend = color_branches(dend, k = 3)
> ht = Heatmap(mat, cluster_rows = dend)
> draw(ht, test = TRUE)
> 
> 
> ht = Heatmap(mat, cluster_columns = FALSE)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, clustering_distance_columns = "pearson")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, clustering_distance_columns = function(x) dist(x))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, clustering_distance_columns = function(x, y) 1 - cor(x, y))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, clustering_method_columns = "single")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_dend_side = "bottom")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_dend_height = unit(4, "cm"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_dend_gp = gpar(lwd = 2, col = "red"))
> draw(ht, test = TRUE)
> 
> dend = as.dendrogram(hclust(dist(t(mat))))
> ht = Heatmap(mat, cluster_columns = dend)
> draw(ht, test = TRUE)
> 
> dend = color_branches(dend, k = 3)
> ht = Heatmap(mat, cluster_columns = dend)
> draw(ht, test = TRUE)
> 
> 
> ### test row/column order
> od = c(seq(1, 24, by = 2), seq(2, 24, by = 2))
> ht = Heatmap(mat, row_order = od)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_order = od, cluster_rows = TRUE)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_order = od)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_order = od, cluster_columns = TRUE)
> draw(ht, test = TRUE)
> 
> 
> #### test row/column names #####
> ht = Heatmap(unname(mat))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, show_row_names = FALSE)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_names_side = "left")
> draw(ht, test = TRUE)
> 
> random_str2 = function(k) {
+ 	sapply(1:k, function(i) paste(sample(letters, sample(5:10, 1)), collapse = ""))
+ }
> ht = Heatmap(mat, row_labels = random_str2(24))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_names_gp = gpar(fontsize = 20))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_names_gp = gpar(fontsize = 1:24/2 + 5))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_names_rot = 45)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_names_rot = 45, row_names_side = "left")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, show_column_names = FALSE)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_names_side = "top")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_labels = random_str2(24))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_names_gp = gpar(fontsize = 20))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_names_gp = gpar(fontsize = 1:24/2 + 5))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_names_rot = 45)
> draw(ht, test = TRUE)
> 
> ### test annotations ####
> anno = HeatmapAnnotation(
+ 	foo = 1:24,
+ 	df = data.frame(type = c(rep("A", 12), rep("B", 12))),
+ 	bar = anno_barplot(24:1))
> ht = Heatmap(mat, top_annotation = anno)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, bottom_annotation = anno)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, top_annotation = anno, bottom_annotation = anno)
> draw(ht, test = TRUE)
> 
> 
> ### test split ####
> ht = Heatmap(mat, km = 3)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 3)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, split = rep(c("A", "B"), times = c(6, 18)))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = rep(c("A", "B"), times = c(6, 18)))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = factor(rep(c("A", "B"), times = c(6, 18)), levels = c("B", "A")))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = rep(c("A", "B"), 12), row_gap = unit(5, "mm"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = data.frame(rep(c("A", "B"), 12), rep(c("C", "D"), each = 12)))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = data.frame(rep(c("A", "B"), 12), rep(c("C", "D"), each = 12)),
+ 	row_gap = unit(c(1, 2, 3), "mm"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 3, row_title = "foo")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 3, row_title = "cluster%s")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 3, row_title = "cluster%s", row_title_rot = 0)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 3, row_title = "cluster%s", row_title_gp = gpar(fill = 2:4, col = "white"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 3, row_title = NULL)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 3, row_names_gp = gpar(col = 2:4))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = rep(c("A", "B"), times = c(6, 18)), row_km = 3)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = rep(c("A", "B"), times = c(6, 18)), row_km = 3, row_title = "cluster%s,group%s", row_title_rot = 0)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = 2)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = 2, row_title = "foo")
> ht = Heatmap(mat, row_split = 2, row_title = "cluster%s")
> 
> 
> dend = as.dendrogram(hclust(dist(mat)))
> ht = Heatmap(mat, cluster_rows = dend, row_split = 2)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = 2, row_names_gp = gpar(col = 2:3))
> draw(ht, test = TRUE)
> 
> 
> ### column split
> ht = Heatmap(mat, column_km = 2)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_km = 2, column_gap = unit(1, "cm"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_split = rep(c("A", "B"), times = c(6, 18)))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_split = data.frame(rep(c("A", "B"), 12), rep(c("C", "D"), each = 12)),
+ 	column_gap = unit(c(1, 2, 3), "mm"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_km = 2, column_title = "foo")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_km = 2, column_title = "cluster%s")
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_km = 2, column_title = "cluster%s", column_title_rot = 90)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_km = 2, column_title = "cluster%s", column_title_gp = gpar(fill = 2:3, col = "white"))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_km = 2, column_title = NULL)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_km = 2, column_names_gp = gpar(col = 2:3))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_split = factor(rep(c("A", "B"), times = c(6, 18)), levels = c("A", "B")), column_km = 2)
> draw(ht, test = TRUE)
> ht = Heatmap(mat, column_split = factor(rep(c("A", "B"), times = c(6, 18)), levels = c("B", "A")), column_km = 2)
> 
> 
> ht = Heatmap(mat, column_split = rep(c("A", "B"), times = c(6, 18)), column_km = 2, 
+ 	column_title = "cluster%s,group%s", column_title_rot = 90)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, column_split = 3)
> draw(ht, test = TRUE)
> 
> dend = as.dendrogram(hclust(dist(t(mat))))
> ht = Heatmap(mat, cluster_columns = dend, column_split = 3)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, top_annotation = anno, bottom_annotation = anno, column_km = 2)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, top_annotation = anno, bottom_annotation = anno, column_split = 3)
> draw(ht, test = TRUE)
> 
> ### combine row and column split
> ht = Heatmap(mat, row_km = 3, column_km = 3)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = 3, column_split = 3)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 3, column_split = 3)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_split = rep(c("A", "B"), 12), 
+ 	column_split = rep(c("C", "D"), 12))
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, top_annotation = anno,
+ 	row_split = rep(c("A", "B"), 12), 
+ 	row_names_gp = gpar(col = 2:3), row_gap = unit(2, "mm"),
+ 	column_split = 3,
+ 	column_names_gp = gpar(col = 2:4), column_gap = unit(4, "mm")
+ )
> draw(ht, test = TRUE)
> 
> 
> #### character matrix
> mat3 = matrix(sample(letters[1:6], 100, replace = TRUE), 10, 10)
> rownames(mat3) = {x = letters[1:10]; x[1] = "aaaaaaaaaaaaaaaaaaaaaaa";x}
> ht = Heatmap(mat3, rect_gp = gpar(col = "white"))
> draw(ht, test = TRUE)
> 
> 
> ### cell_fun
> mat = matrix(1:9, 3, 3)
> rownames(mat) = letters[1:3]
> colnames(mat) = letters[1:3]
> 
> ht = Heatmap(mat, rect_gp = gpar(col = "white"), cell_fun = function(j, i, x, y, width, height, fill) grid.text(mat[i, j], x = x, y = y),
+ 	cluster_rows = FALSE, cluster_columns = FALSE, row_names_side = "left", column_names_side = "top",
+ 	column_names_rot = 0)
> draw(ht, test = TRUE)
> 
> 
> ### test the size
> ht = Heatmap(mat)
> ht = prepare(ht)
> ht@heatmap_param[c("width", "height")]
$width
[1] 1npc

$height
[1] 1npc

> ht@matrix_param[c("width", "height")]
$width
[1] 3null

$height
[1] 3null

> 
> ht = Heatmap(mat, width = unit(10, "cm"), height = unit(10, "cm"))
> ht = prepare(ht)
> ht@heatmap_param[c("width", "height")]
$width
[1] 114.853733333333mm

$height
[1] 114.853733333333mm

> ht@matrix_param[c("width", "height")]
$width
[1] 10cm

$height
[1] 10cm

> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, width = unit(10, "cm"))
> ht = prepare(ht)
> ht@heatmap_param[c("width", "height")]
$width
[1] 114.853733333333mm

$height
[1] 1npc

> ht@matrix_param[c("width", "height")]
$width
[1] 10cm

$height
[1] 3null

> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, heatmap_width = unit(10, "cm"), heatmap_height = unit(10, "cm"))
> ht = prepare(ht)
> ht@heatmap_param[c("width", "height")]
$width
[1] 10cm

$height
[1] 10cm

> ht@matrix_param[c("width", "height")]
$width
[1] 85.1462666666667mm

$height
[1] 85.1462666666667mm

> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, heatmap_width = unit(10, "cm"))
> ht = prepare(ht)
> ht@heatmap_param[c("width", "height")]
$width
[1] 10cm

$height
[1] 1npc

> ht@matrix_param[c("width", "height")]
$width
[1] 85.1462666666667mm

$height
[1] 3null

> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, use_raster = TRUE)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 2, use_raster = TRUE)
> draw(ht, test = TRUE)
> 
> ht = Heatmap(mat, row_km = 2, column_km = 2, use_raster = TRUE)
> draw(ht, test = TRUE)
> 
> #### test global padding
> ra = rowAnnotation(foo = 1:3)
> ht = Heatmap(mat, show_column_names = FALSE) + ra
> draw(ht)
> 
> ht = Heatmap(matrix(rnorm(100), 10), row_km = 2, row_title = "")
> draw(ht)
> 
> if(0) {
+ ht = Heatmap(matrix(rnorm(100), 10), heatmap_width = unit(5, "mm"))
+ draw(ht)
+ }
> 
> proc.time()
   user  system elapsed 
  17.84    0.95   18.34 

ComplexHeatmap.Rcheck/tests/test-Heatmap-cluster.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> # ht_opt("verbose" = TRUE)
> m = matrix(rnorm(50), nr = 10)
> 
> ht = Heatmap(m)
> ht = make_row_cluster(ht)
> 
> ht = Heatmap(m, cluster_rows = FALSE)
> ht = make_row_cluster(ht)
> 
> ht = Heatmap(m, row_km = 2)
> ht = make_row_cluster(ht)
> 
> ht = Heatmap(m, row_split = sample(letters[1:2], 10, replace = TRUE))
> ht = make_row_cluster(ht)
> 
> ht = Heatmap(m, cluster_rows = hclust(dist(m)))
> ht = make_row_cluster(ht)
> 
> ht = Heatmap(m, cluster_rows = hclust(dist(m)), row_split = 2)
> ht = make_row_cluster(ht)
> 
> # ht_opt("verbose" = FALSE)
> 
> proc.time()
   user  system elapsed 
   1.89    0.32    2.07 

ComplexHeatmap.Rcheck/tests/test-HeatmapAnnotation.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> 
> ha = HeatmapAnnotation(foo = 1:10)
> ha
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_0 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  6.75733333333333mm extension on the right 

 name   annotation_type color_mapping height
  foo continuous vector        random    5mm
> 
> 
> ha = HeatmapAnnotation(foo = cbind(1:10, 10:1))
> ha
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_1 
  position: column 
  items: 10 
  width: 1npc 
  height: 10mm 
  this object is subsettable
  6.75733333333333mm extension on the right 

 name   annotation_type color_mapping height
  foo continuous matrix        random   10mm
> draw(ha, test = "matrix as column annotation")
> 
> ha = HeatmapAnnotation(foo = 1:10, bar = sample(c("a", "b"), 10, replace = TRUE),
+ 	pt = anno_points(1:10), annotation_name_side = "left")
> draw(ha, test = "complex annotations")
> 
> ha = HeatmapAnnotation(foo = 1:10, bar = sample(c("a", "b"), 10, replace = TRUE),
+ 	pt = anno_points(1:10), annotation_name_side = "left", height = unit(8, "cm"))
> draw(ha, test = "complex annotations")
> 
> 
> ha = HeatmapAnnotation(foo = 1:10, bar = sample(c("a", "b"), 10, replace = TRUE))
> 
> ha = HeatmapAnnotation(foo = 1:10, 
+ 	bar = cbind(1:10, 10:1),
+ 	pt = anno_points(1:10),
+ 	gap = unit(2, "mm"))
> draw(ha, test = "complex annotations")
> 
> ha2 = re_size(ha, annotation_height = unit(1:3, "cm"))
> draw(ha2, test = "complex annotations")
> ha2 = re_size(ha, annotation_height = 1, height = unit(6, "cm"))
> draw(ha2, test = "complex annotations")
> ha2 = re_size(ha, annotation_height = 1:3, height = unit(6, "cm"))
> draw(ha2, test = "complex annotations")
> ha2 = re_size(ha, annotation_height = unit(c(1, 2, 3), c("null", "null", "cm")), height = unit(6, "cm"))
> draw(ha2, test = "complex annotations")
> ha2 = re_size(ha, annotation_height = unit(c(2, 2, 3), c("cm", "null", "cm")), height = unit(6, "cm"))
> draw(ha2, test = "complex annotations")
> ha2 = re_size(ha, annotation_height = unit(c(2, 2, 3), c("cm", "cm", "cm")))
> draw(ha2, test = "complex annotations")
> ha2 = re_size(ha[, 1:2], annotation_height = 1, height = unit(4, "cm"))
> draw(ha2, test = "complex annotations")
> ha2 = re_size(ha[, 1:2], annotation_height = c(1, 4), height = unit(4, "cm"))
> draw(ha2, test = "complex annotations")
> ha2 = re_size(ha[, 1:2], height = unit(6, "cm"))
> draw(ha2, test = "complex annotations")
> 
> ha2 = re_size(ha, height = unit(6, "cm"))
> draw(ha2, test = "complex annotations")
> 
> #### test anno_empty and self-defined anotation function
> ha = HeatmapAnnotation(foo = anno_empty(), height = unit(4, "cm"))
> draw(ha, 1:10, test = "anno_empty")
> ha = HeatmapAnnotation(foo = anno_empty(), bar = 1:10, height = unit(4, "cm"))
> draw(ha, 1:10, test = "anno_empty")
> ha = HeatmapAnnotation(foo = anno_empty(), bar = 1:10, height = unit(4, "cm"))
> draw(ha, 1:10, test = "anno_empty")
> 
> ha = HeatmapAnnotation(foo = function(index) {grid.rect()}, bar = 1:10, height = unit(4, "cm"))
> draw(ha, 1:10, test = "self-defined function")
> 
> 
> lt = lapply(1:10, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
> ha = HeatmapAnnotation(foo = 1:10, bar = sample(c("a", "b"), 10, replace = TRUE),
+ 	anno = anno_horizon(lt), which = "row")
> draw(ha, test = "complex annotations on row")
> 
> ## test row annotation with no heatmap
> rowAnnotation(foo = 1:10, bar = anno_points(10:1))
A HeatmapAnnotation object with 2 annotations
  name: heatmap_annotation_11 
  position: row 
  items: 10 
  width: 15.3514598035146mm 
  height: 1npc 
  this object is subsettable
  9.17784444444445mm extension on the bottom 

 name   annotation_type color_mapping width
  foo continuous vector        random   5mm
  bar     anno_points()                10mm
> 
> if(0) {
+ HeatmapAnnotation(1:10)
+ 
+ HeatmapAnnotation(data.frame(1:10))
+ }
> 
> 
> ha = HeatmapAnnotation(summary = anno_summary(height = unit(4, "cm")))
> v = sample(letters[1:2], 50, replace = TRUE)
> split = sample(letters[1:2], 50, replace = TRUE)
> 
> ht = Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)
> draw(ht)
> 
> ha = HeatmapAnnotation(summary = anno_summary(gp = gpar(fill = 2:3), height = unit(4, "cm")))
> v = rnorm(50)
> ht = Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)
> draw(ht)
> 
> 
> ### auto adjust
> m = matrix(rnorm(100), 10)
> ht_list = Heatmap(m, top_annotation = HeatmapAnnotation(foo = 1:10), column_dend_height = unit(4, "cm")) +
+ 	Heatmap(m, top_annotation = HeatmapAnnotation(bar = anno_points(1:10)),
+ 		cluster_columns = FALSE)
> draw(ht_list)
> 
> fun = function(index) {
+ 	grid.rect()
+ }
> ha = HeatmapAnnotation(fun = fun, height = unit(4, "cm"))
> draw(ha, 1:10, test = TRUE)
> 
> ha = rowAnnotation(fun = fun, width = unit(4, "cm"))
> draw(ha, 1:10, test = TRUE)
> 
> 
> ## test anno_mark
> m = matrix(rnorm(1000), nrow = 100)
> ha1 = rowAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]))
> ht = Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha1)
> draw(ht)
> ht = Heatmap(m, name = "mat", cluster_rows = FALSE) + ha1
> draw(ht)
> 
> split = rep("a", 100); split[c(1:4, 20, 60, 98:100)] = "b"
> ht = Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha1, row_split = split, gap = unit(1, "cm"))
> draw(ht)
> ht = Heatmap(m, name = "mat", cluster_rows = FALSE, row_split = split, gap = unit(1, "cm")) + ha1
> draw(ht)
> 
> # ha has two annotations
> ha2 = rowAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]), bar = 1:100)
> ht = Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha2)
> draw(ht)
> ht = Heatmap(m, name = "mat", cluster_rows = FALSE) + ha2
> draw(ht)
> 
> ht = Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha2, row_split = split, gap = unit(1, "cm"))
> draw(ht)
> ht = Heatmap(m, name = "mat", cluster_rows = FALSE, row_split = split, gap = unit(1, "cm")) + ha2
> draw(ht)
> 
> ## test anno_mark as column annotation
> m = matrix(rnorm(1000), ncol = 100)
> ha1 = columnAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]))
> ht = Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha1)
> draw(ht)
> ht_list = ha1 %v% Heatmap(m, name = "mat", cluster_columns = FALSE)
> draw(ht_list)
> 
> split = rep("a", 100); split[c(1:4, 20, 60, 98:100)] = "b"
> ht = Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha1, column_split = split, column_gap = unit(1, "cm"))
> draw(ht)
> ht_list = ha1 %v% Heatmap(m, name = "mat", cluster_columns = FALSE, column_split = split, gap = unit(1, "cm"))
> draw(ht_list)
> 
> # ha has two annotations
> ha2 = HeatmapAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]), bar = 1:100)
> ht = Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha2)
> draw(ht)
> ht_list = ha2 %v% Heatmap(m, name = "mat", cluster_columns = FALSE)
> draw(ht_list)
> 
> ht = Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha2, column_split = split, column_gap = unit(1, "cm"))
> draw(ht)
> ht_list = ha2 %v% Heatmap(m, name = "mat", cluster_columns = FALSE, column_split = split, column_gap = unit(1, "cm"))
> draw(ht_list)
> 
> 
> ### when there are only simple annotations
> col_fun = colorRamp2(c(0, 10), c("white", "blue"))
> ha = HeatmapAnnotation(
+     foo = cbind(a = 1:10, b = 10:1), 
+     bar = sample(letters[1:3], 10, replace = TRUE),
+     col = list(foo = col_fun,
+                bar = c("a" = "red", "b" = "green", "c" = "blue")
+     ),
+     simple_anno_size = unit(1, "cm")
+ )
> draw(ha, test = TRUE)
> 
> set.seed(123)
> mat1 = matrix(rnorm(80, 2), 8, 10)
> mat1 = rbind(mat1, matrix(rnorm(40, -2), 4, 10))
> rownames(mat1) = paste0("R", 1:12)
> colnames(mat1) = paste0("C", 1:10)
> 
> mat2 = matrix(runif(60, max = 3, min = 1), 6, 10)
> mat2 = rbind(mat2, matrix(runif(60, max = 2, min = 0), 6, 10))
> rownames(mat2) = paste0("R", 1:12)
> colnames(mat2) = paste0("C", 1:10)
> 
> ind = sample(12, 12)
> mat1 = mat1[ind, ]
> mat2 = mat2[ind, ]
> 
> ha1 = HeatmapAnnotation(foo1 = 1:10, 
+ 	                    annotation_height = unit(1, "cm"),
+ 	                    simple_anno_size_adjust = TRUE,
+                         annotation_name_side = "left")
> ha2 = HeatmapAnnotation(df = data.frame(foo1 = 1:10,
+                                         foo2 = 1:10,
+                                         foo4 = 1:10,
+                                         foo5 = 1:10))
> ht1 = Heatmap(mat1, name = "rnorm", top_annotation = ha1)
> ht2 = Heatmap(mat2, name = "runif", top_annotation = ha2)
> 
> draw(ht1 + ht2)
> 
> ##### test size of a single simple annotation
> 
> ha = HeatmapAnnotation(foo1 = 1:10, 
+ 	simple_anno_size = unit(1, "cm")
+ )
> ha = HeatmapAnnotation(foo1 = 1:10, 
+ 	annotation_height = unit(1, "cm"),
+ 	simple_anno_size_adjust = TRUE
+ )
> ha = HeatmapAnnotation(foo1 = 1:10, 
+ 	height = unit(1, "cm"),
+ 	simple_anno_size_adjust = TRUE
+ )
> 
> 
> ## annotation with the same names
> 
> set.seed(123)
> m = matrix(rnorm(100), 10)
> ha1 = HeatmapAnnotation(foo = sample(c("a", "b"), 10, replace = TRUE))
> ha2 = HeatmapAnnotation(foo = sample(c("b", "c"), 10, replace = TRUE))
> 
> ht_list = Heatmap(m, top_annotation = ha1) + 
+ 	Heatmap(m, top_annotation = ha2)
> draw(ht_list)
> 
> ha1 = HeatmapAnnotation(foo = sample(c("a", "b"), 10, replace = TRUE),
+ 	annotation_legend_param = list(
+ 		foo = list(title = "letters", 
+ 			       at = c("a", "b", "c"),
+ 			       labels = c("A", "B", "C")
+ 			  )
+ 	))
> ha2 = HeatmapAnnotation(foo = sample(c("b", "c"), 10, replace = TRUE))
> 
> ht_list = Heatmap(m, top_annotation = ha1) + 
+ 	Heatmap(m, top_annotation = ha2)
> draw(ht_list)
> 
> x = matrix(rnorm(6), ncol=3)
> subtype_col = c("Basal" = "purple","Her2" = "black","Normal" = "blue")
> h1 <- HeatmapAnnotation("Subtype" = c("Basal","Her2", "Normal"),
+                         col = list("Subtype" = subtype_col))
> h2 <- HeatmapAnnotation("Subtype" = c("Normal","Normal", "Basal"),
+                         col = list("Subtype" = subtype_col))
> 
> ht_list = Heatmap(x,top_annotation = h1) + Heatmap(x,top_annotation = h2)
> draw(ht_list)
> 
> 
> ### test annotation_label
> ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],
+ 	annotation_label = c("anno1", "anno2"))
> draw(ha, test = TRUE)
> 
> ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],
+ 	annotation_label = list(foo = "anno1"))
> draw(ha, test = TRUE)
> 
> 
> ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],
+ 	annotation_label = list(
+ 		foo = gt_render("foo", gp = gpar(box_fill = "red"))))
Loading required namespace: gridtext
> draw(ha, test = TRUE)
> 
> ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],
+ 	annotation_label = list(
+ 		foo = gt_render("foo", gp = gpar(box_fill = "red")),
+ 		bar = gt_render("bar", gp = gpar(box_fill = "blue"))))
> draw(ha, test = TRUE)
> 
> 
> ### test whether arguments can be captured
> HeatmapAnnotation(a = 1:10)
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_38 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm
> rowAnnotation(a = 1:10)
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_39 
  position: row 
  items: 10 
  width: 5mm 
  height: 1npc 
  this object is subsettable
  3.35373333333333mm extension on the bottom 

 name   annotation_type color_mapping width
    a continuous vector        random   5mm
> columnAnnotation(a = 1:10)
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_40 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm
> do.call(HeatmapAnnotation, list(a = 1:10))
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_41 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm
> do.call(rowAnnotation, list(a = 1:10))
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_42 
  position: row 
  items: 10 
  width: 5mm 
  height: 1npc 
  this object is subsettable
  3.35373333333333mm extension on the bottom 

 name   annotation_type color_mapping width
    a continuous vector        random   5mm
> do.call(columnAnnotation, list(a = 1:10))
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_43 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm
> do.call("HeatmapAnnotation", list(a = 1:10))
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_44 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm
> do.call("rowAnnotation", list(a = 1:10))
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_45 
  position: row 
  items: 10 
  width: 5mm 
  height: 1npc 
  this object is subsettable
  3.35373333333333mm extension on the bottom 

 name   annotation_type color_mapping width
    a continuous vector        random   5mm
> do.call("columnAnnotation", list(a = 1:10))
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_46 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm
> 
> f = function() HeatmapAnnotation(a = 1:10)
> f()
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_47 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm
> f = function() rowAnnotation(a = 1:10)
> f()
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_48 
  position: row 
  items: 10 
  width: 5mm 
  height: 1npc 
  this object is subsettable
  3.35373333333333mm extension on the bottom 

 name   annotation_type color_mapping width
    a continuous vector        random   5mm
> f = function() columnAnnotation(a = 1:10)
> f()
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_49 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm
> 
> sapply(1, function(x) HeatmapAnnotation(a = 1:10))
[[1]]
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_50 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm

> sapply(1, function(x) rowAnnotation(a = 1:10))
[[1]]
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_51 
  position: row 
  items: 10 
  width: 5mm 
  height: 1npc 
  this object is subsettable
  3.35373333333333mm extension on the bottom 

 name   annotation_type color_mapping width
    a continuous vector        random   5mm

> sapply(1, function(x) columnAnnotation(a = 1:10))
[[1]]
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_52 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm

> 
> mapply(function(x, y) HeatmapAnnotation(a = 1:10), list(1), list(1))
[[1]]
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_53 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm

> mapply(function(x, y) rowAnnotation(a = 1:10), list(1), list(1))
[[1]]
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_54 
  position: row 
  items: 10 
  width: 5mm 
  height: 1npc 
  this object is subsettable
  3.35373333333333mm extension on the bottom 

 name   annotation_type color_mapping width
    a continuous vector        random   5mm

> mapply(function(x, y) columnAnnotation(a = 1:10), list(1), list(1))
[[1]]
A HeatmapAnnotation object with 1 annotation
  name: heatmap_annotation_55 
  position: column 
  items: 10 
  width: 1npc 
  height: 5mm 
  this object is subsettable
  3.35373333333333mm extension on the right 

 name   annotation_type color_mapping height
    a continuous vector        random    5mm

> 
> 
> try({
+ 	HeatmapAnnotation(1:10)
+ 	HeatmapAnnotation(df = data.frame(a = 1:10), a = 1:10)
+ })
Error : The annotation should be specified as name-value pairs or via argument
`df` with a data frame.
> 
> proc.time()
   user  system elapsed 
  10.93    0.81   11.29 

ComplexHeatmap.Rcheck/tests/test-HeatmapList-class.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> set.seed(123)
> nr1 = 10; nr2 = 8; nr3 = 6
> nc1 = 6; nc2 = 8; nc3 = 10
> mat1 = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1,   sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc1, mean = 0,   sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc1, mean = 0,   sd = 0.5), nr = nr3)),
+     rbind(matrix(rnorm(nr1*nc2, mean = 0,   sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc2, mean = 1,   sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc2, mean = 0,   sd = 0.5), nr = nr3)),
+     rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc3, mean = 1,   sd = 0.5), nr = nr3))
+    )
> 
> rownames(mat1) = paste0("row_1_", seq_len(nrow(mat1)))
> colnames(mat1) = paste0("column_1_", seq_len(nrow(mat1)))
> 
> nr3 = 10; nr1 = 8; nr2 = 6
> nc3 = 6; nc1 = 8; nc2 = 10
> mat2 = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1,   sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc1, mean = 0,   sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc1, mean = 0,   sd = 0.5), nr = nr3)),
+     rbind(matrix(rnorm(nr1*nc2, mean = 0,   sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc2, mean = 1,   sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc2, mean = 0,   sd = 0.5), nr = nr3)),
+     rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
+           matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
+           matrix(rnorm(nr3*nc3, mean = 1,   sd = 0.5), nr = nr3))
+    )
> 
> rownames(mat2) = paste0("row_2_", seq_len(nrow(mat2)))
> colnames(mat2) = paste0("column_2_", seq_len(nrow(mat2)))
> 
> 
> ht_list = Heatmap(mat1) + Heatmap(mat2)
> draw(ht_list)
> 
> ######### legend ############
> draw(ht_list, heatmap_legend_side = "bottom")
> draw(ht_list, heatmap_legend_side = "left")
> draw(ht_list, heatmap_legend_side = "top")
> 
> 
> ########## width #############
> ht_list = Heatmap(mat1, width = unit(6, "cm")) + Heatmap(mat2)
> draw(ht_list)
> ht_list = Heatmap(mat1) + Heatmap(mat2, width = unit(8, "cm"))
> draw(ht_list)
> ht_list = Heatmap(mat1, width = unit(12, "cm")) + Heatmap(mat2, width = unit(8, "cm"))
> draw(ht_list)
> 
> ht_list = Heatmap(mat1, width = unit(6, "cm")) + Heatmap(mat2)
> draw(ht_list)
> ht_list = Heatmap(mat1) + Heatmap(mat2, width = unit(6, "cm"))
> draw(ht_list)
> ht_list = Heatmap(mat1, width = unit(6, "cm")) + Heatmap(mat2, width = unit(6, "cm"))
> draw(ht_list)
> ht_list = Heatmap(mat1, width = 4) + Heatmap(mat2)
> draw(ht_list)
> ht_list = Heatmap(mat1, width = 2) + Heatmap(mat2, width = 1)
> draw(ht_list)
> 
> 
> ########### height ###########
> ht_list = Heatmap(mat1, height = unit(6, "cm")) + Heatmap(mat2)
> draw(ht_list)
> ht_list = Heatmap(mat1, heatmap_height = unit(6, "cm")) + Heatmap(mat2)
> draw(ht_list)
> ht_list = Heatmap(mat1, width = unit(6, "cm"), height = unit(6, "cm")) + 
+ 	Heatmap(mat2, width = unit(6, "cm"), height = unit(6, "cm"))
> draw(ht_list, column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
> 
> ##### split #####
> ht_list = Heatmap(mat1, name = "m1", row_km = 2) + Heatmap(mat2, name = "m2", row_km = 3)
> draw(ht_list, main_heatmap = "m1")
> draw(ht_list, main_heatmap = "m2")
> 
> ht_list = Heatmap(mat1, name = "m1", row_km = 2, column_km = 3, width = unit(8, "cm"), height = unit(6, "cm")) + 
+ 	Heatmap(mat2, name = "m2", row_km = 3, column_km = 2, width = unit(8, "cm"), height = unit(10, "cm"))
> draw(ht_list, main_heatmap = "m1", column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
> draw(ht_list, main_heatmap = "m2", column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
> 
> ##### adjust column annotations #####
> ha1 = HeatmapAnnotation(foo = 1:24, bar = anno_points(24:1, height = unit(4, "cm")))
> ha2 = HeatmapAnnotation(bar = anno_points(24:1), foo = 1:24)
> ht_list = Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2, top_annotation = ha2)
> draw(ht_list)
> ha2 = HeatmapAnnotation(foo = 1:24)
> ht_list = Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2, top_annotation = ha2)
> draw(ht_list)
> ht_list = Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2)
> draw(ht_list)
> ht_list = Heatmap(mat1, bottom_annotation = ha1) + Heatmap(mat2)
> draw(ht_list)
> 
> 
> #### row annotations #####
> ha = rowAnnotation(foo = 1:24, bar = anno_points(24:1), width = unit(6, "cm"))
> ht_list = Heatmap(mat1) + ha
> draw(ht_list)
> ht_list = Heatmap(mat1, width = unit(6, "cm")) + ha
> draw(ht_list)
> ht_list = Heatmap(mat1, width = unit(6, "cm"), row_km = 2) + ha
> draw(ht_list)
> 
> ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") +
+   rowAnnotation(foo = 1:10, bar = anno_points(10:1)) + 
+   Heatmap(matrix(runif(100), 10), name = "runif")
> summary(ht_list[1:5, ])
A horizontal heamtap list with 3 heatmap/annotations.
  rnorm: a matrix with 5 rows and 10 columns
  heatmap_annotation_4: a list of 2 annotations
    foo:   a simple annotation.
    bar:   a complex annotation.
  runif: a matrix with 5 rows and 10 columns
> summary(ht_list[1:5, 1])
A horizontal heamtap list with 1 heatmap/annotations.
  rnorm: a matrix with 5 rows and 10 columns
> summary(ht_list[1:5, "rnorm"])
A horizontal heamtap list with 1 heatmap/annotations.
  rnorm: a matrix with 5 rows and 10 columns
> summary(ht_list[1:5, c("rnorm", "foo")])
A horizontal heamtap list with 2 heatmap/annotations.
  rnorm: a matrix with 5 rows and 10 columns
  heatmap_annotation_4: a list of 1 annotations
    foo:   a simple annotation.
> 
> ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") %v%
+   columnAnnotation(foo = 1:10, bar = anno_points(10:1)) %v%
+   Heatmap(matrix(runif(100), 10), name = "runif")
> summary(ht_list[, 1:5])
A vertical heamtap list with 3 heatmap/annotations.
  rnorm: a matrix with 10 rows and 5 columns
  heatmap_annotation_5: a list of 2 annotations
    foo:   a simple annotation.
    bar:   a complex annotation.
  runif: a matrix with 10 rows and 5 columns
> summary(ht_list[1, 1:5])
A vertical heamtap list with 1 heatmap/annotations.
  rnorm: a matrix with 10 rows and 5 columns
> summary(ht_list["rnorm", 1:5])
A vertical heamtap list with 1 heatmap/annotations.
  rnorm: a matrix with 10 rows and 5 columns
> summary(ht_list[c("rnorm", "foo"), 1:5])
A vertical heamtap list with 2 heatmap/annotations.
  rnorm: a matrix with 10 rows and 5 columns
  heatmap_annotation_5: a list of 1 annotations
    foo:   a simple annotation.
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  12.78    0.89   13.35 

ComplexHeatmap.Rcheck/tests/test-interactive.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> if(0) {
+ 
+ m = matrix(rnorm(100), 10)
+ rownames(m) = 1:10
+ colnames(m) = 1:10
+ 
+ ht = Heatmap(m)
+ ht = draw(ht)
+ selectArea(ht)
+ 
+ 
+ 
+ ht = Heatmap(m, row_km = 2, column_km = 2)
+ ht = draw(ht)
+ selectArea(ht)
+ 
+ 
+ ht = Heatmap(m, row_km = 2, column_km = 2) + Heatmap(m, row_km = 2, column_km = 2)
+ ht = draw(ht)
+ selectArea(ht)
+ 
+ pdf("~/test.pdf")
+ ht = Heatmap(m)
+ ht = draw(ht)
+ selectArea(ht, pos1 = unit(c(1, 1), "cm"), pos2 = unit(c(4, 4), "cm"), verbose = TRUE)
+ 
+ set.seed(123)
+ ht = Heatmap(m, row_km = 2, column_km = 2)
+ ht = draw(ht)
+ selectArea(ht, pos1 = unit(c(1, 1), "cm"), pos2 = unit(c(8, 8), "cm"), verbose = TRUE)
+ dev.off()
+ 
+ png("~/test-1.png")
+ ht = Heatmap(m)
+ ht = draw(ht)
+ selectArea(ht, pos1 = unit(c(1, 1), "cm"), pos2 = unit(c(4, 4), "cm"), verbose = TRUE)
+ dev.off()
+ 
+ png("~/test-2.png")
+ set.seed(123)
+ ht = Heatmap(m, row_km = 2, column_km = 2)
+ ht = draw(ht)
+ selectArea(ht, pos1 = unit(c(1, 1), "cm"), pos2 = unit(c(8, 8), "cm"), verbose = TRUE)
+ dev.off()
+ 
+ }
> 
> proc.time()
   user  system elapsed 
   0.14    0.04    0.17 

ComplexHeatmap.Rcheck/tests/test-Legend.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> if(!exists("random_str")) {
+ 	random_str = ComplexHeatmap:::random_str
+ }
> 
> lgd = Legend(at = 1:6, legend_gp = gpar(fill = 1:6))
> draw(lgd, test = "default discrete legends style")
> 
> lgd = Legend(labels = 1:6, legend_gp = gpar(fill = 1:6))
> draw(lgd, test = "only specify labels with no at")
> 
> 
> lgd = Legend(labels = month.name[1:6], title = "foo", legend_gp = gpar(fill = 1:6))
> draw(lgd, test = "add labels and title")
> 
> lgd = Legend(labels = month.name[1:6], title = "foo", legend_gp = gpar(fill = 1:6),
+ 	title_position = "lefttop")
> draw(lgd, test = "title put in the lefttop")
> 
> lgd = Legend(labels = month.name[1:6], title = "foo", legend_gp = gpar(fill = 1:6),
+ 	title_position = "lefttop-rot")
> draw(lgd, test = "title put in the lefttop-rot")
> 
> lgd = Legend(labels = month.name[1:6], title = "foo", legend_gp = gpar(fill = 1:6),
+ 	title_position = "leftcenter-rot")
> draw(lgd, test = "title put in the leftcenter-rot")
> 
> lgd = Legend(labels = 1:6, title = "fooooooo", legend_gp = gpar(fill = 1:6))
> draw(lgd, test = "title is longer than the legend body")
> 
> lgd = Legend(at = 1:6, legend_gp = gpar(fill = 1:6), grid_height = unit(1, "cm"), 
+ 	title = "foo", grid_width = unit(5, "mm"))
> draw(lgd, test = "grid size")
> 
> lgd = Legend(labels = month.name[1:6], legend_gp = gpar(fill = 1:6), title = "foo", 
+ 	labels_gp = gpar(col = "red", fontsize = 14))
> draw(lgd, test = "labels_gp")
> 
> lgd = Legend(labels = month.name[1:6], legend_gp = gpar(fill = 1:6), title = "foo", 
+ 	title_gp = gpar(col = "red", fontsize = 14))
> draw(lgd, test = "title_gp")
> 
> lgd = Legend(labels = month.name[1:6], legend_gp = gpar(fill = 1:6), title = "foo", 
+ 	border = "red")
> draw(lgd, test = "legend border")
> 
> lgd = Legend(labels = month.name[1:10], legend_gp = gpar(fill = 1:10), title = "foo", 
+ 	ncol = 3)
> draw(lgd, test = "in 3 columns")
> 
> lgd = Legend(labels = month.name[1:10], legend_gp = gpar(fill = 1:10), title = "foo", 
+ 	ncol = 3, title_position = "topcenter")
> draw(lgd, test = "in 3 columns, title in the center")
> 
> lgd = Legend(labels = month.name[1:10], legend_gp = gpar(fill = 1:10), title = "foo", 
+ 	ncol = 3, by_row = TRUE)
> draw(lgd, test = "in 3 columns and by rows")
> 
> lgd = Legend(labels = month.name[1:10], legend_gp = gpar(fill = 1:10), title = "foo", 
+ 	ncol = 3, gap = unit(1, "cm"))
> draw(lgd, test = "in 3 columns with gap between columns")
> 
> lgd = Legend(labels = month.name[1:10], legend_gp = gpar(fill = 1:10), title = "foo", 
+ 	nrow = 3)
> draw(lgd, test = "in 3 rows")
> 
> lgd = Legend(labels = month.name[1:6], legend_gp = gpar(fill = 1:6), title = "foooooo", 
+ 	nrow = 1, title_position = "lefttop")
> draw(lgd, test = "1 row and title is on the left")
> 
> lgd = Legend(labels = month.name[1:6], legend_gp = gpar(fill = 1:6), title = "foooooo", 
+ 	nrow = 1, title_position = "lefttop-rot")
> draw(lgd, test = "1 row and title is on the left, 90 rotation")
> 
> lgd = Legend(labels = month.name[1:6], legend_gp = gpar(fill = 1:6), title = "foooooo", 
+ 	nrow = 1, title_position = "leftcenter")
> draw(lgd, test = "1 row and title is on the left, 90 rotation")
> 
> lgd = Legend(labels = month.name[1:6], title = "foo", type = "points", pch = 1:6, 
+ 	legend_gp = gpar(col = 1:6), background = "red")
> draw(lgd, test = "points as legends")
> 
> lgd = Legend(labels = month.name[1:6], title = "foo", type = "points", pch = letters[1:6], 
+ 	legend_gp = gpar(col = 1:6), background = "white")
> draw(lgd, test = "letters as legends")
> 
> lgd = Legend(labels = month.name[1:6], title = "foo", type = "lines", 
+ 	legend_gp = gpar(col = 1:6, lty = 1:6))
> draw(lgd, test = "lines as legends")
> 
> ###### vertical continous legend #######
> col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
> lgd = Legend(col_fun = col_fun, title = "foo")
> draw(lgd, test = "only col_fun")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.25, 0.5, 0.75, 1))
> draw(lgd, test = "with at")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = rev(c(0, 0.25, 0.5, 0.75, 1)))
> draw(lgd, test = "with at")
> 
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.5, 1), labels = c("low", "median", "high"))
> draw(lgd, test = "with labels")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", legend_height = unit(6, "cm"))
> draw(lgd, test = "set legend_height")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", labels_gp = gpar(col = "red"))
> draw(lgd, test = "set label color")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", border = "red")
> draw(lgd, test = "legend border")
> 
> lgd = Legend(col_fun = col_fun, title = "foooooooo", title_position = "lefttop-rot")
> draw(lgd, test = "lefttop rot title")
> 
> lgd = Legend(col_fun = col_fun, title = "foooooooo", title_position = "leftcenter-rot")
> draw(lgd, test = "leftcenter top title")
> 
> 
> lgd = Legend(col_fun = col_fun, title = "foo", title_position = "lefttop", direction = "horizontal")
> draw(lgd, test = "lefttop title")
> 
> ###### horizontal continous legend #######
> col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
> lgd = Legend(col_fun = col_fun, title = "foo", direction = "horizontal")
> draw(lgd, test = "only col_fun")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.25, 0.5, 0.75, 1), direction = "horizontal")
> draw(lgd, test = "with at")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = rev(c(0, 0.25, 0.5, 0.75, 1)), direction = "horizontal")
> draw(lgd, test = "with at")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.5, 1), labels = c("low", "median", "high"),
+ 	direction = "horizontal")
> draw(lgd, test = "with labels")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", legend_width = unit(6, "cm"), direction = "horizontal")
> draw(lgd, test = "set legend_width")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", labels_gp = gpar(col = "red"), direction = "horizontal")
> draw(lgd, test = "set label color")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", border = "red", direction = "horizontal")
> draw(lgd, test = "legend border")
> 
> lgd = Legend(col_fun = col_fun, title = "foooooooo", direction = "horizontal", 
+ 	title_position = "topcenter")
> draw(lgd, test = "topcenter title")
> 
> lgd = Legend(col_fun = col_fun, title = "foooooooo", direction = "horizontal", 
+ 	title_position = "lefttop")
> draw(lgd, test = "lefttop title")
> 
> lgd = Legend(col_fun = col_fun, title = "foooooooo", direction = "horizontal", 
+ 	title_position = "leftcenter")
> draw(lgd, test = "leftcenter title")
> 
> 
> ###### pack legend
> lgd1 = Legend(at = 1:6, legend_gp = gpar(fill = 1:6), title = "legend1")
> lgd2 = Legend(col_fun = col_fun, title = "legend2", at = c(0, 0.25, 0.5, 0.75, 1))
> 
> pd = packLegend(lgd1, lgd2)
> draw(pd, test = "two legends")
> 
> pd = packLegend(list = list(lgd1, lgd2))
> draw(pd, test = "two legends specified as a list")
> 
> pd = packLegend(lgd1, lgd2, direction = "horizontal")
> draw(pd, test = "two legends packed horizontally")
> 
> lgd3 = Legend(at = 1:6, legend_gp = gpar(fill = 1:6), title = "legend1")
> lgd4 = Legend(col_fun = col_fun, title = "legend2", at = c(0, 0.25, 0.5, 0.75, 1), direction = "horizontal")
> pd = packLegend(lgd3, lgd4)
> draw(pd, test = "two legends with different directions")
> pd = packLegend(lgd3, lgd4, direction = "horizontal")
> draw(pd, test = "two legends with different directions")
> 
> pd = packLegend(lgd1, lgd2, lgd1, lgd2)
> draw(pd, test = "many legends with same legends")
> 
> lgd3 = Legend(at = 1:6, legend_gp = gpar(fill = 1:6), title = "legend1")
> lgd4 = Legend(col_fun = col_fun, title = "legend2", at = c(0, 0.25, 0.5, 0.75, 1))
> pd = packLegend(lgd1, lgd2, lgd3, lgd4)
> draw(pd, test = "many legends with all different legends")
> 
> pd = packLegend(lgd1, lgd2, lgd1, lgd2, lgd1, lgd2)
> draw(pd, test = "many legends")
> 
> pd = packLegend(lgd1, lgd2, lgd1, lgd2, lgd1, lgd2, max_height = unit(1, "npc"))
> draw(pd, test = "many legends, max_height = unit(1, 'npc')")
> ## reduce the height of the interactive window and rerun draw()
> 
> pd = packLegend(lgd1, lgd2, lgd1, lgd2, lgd1, lgd2, max_height = unit(10, "cm"))
> draw(pd, test = "many legends, max_height = unit(10, 'cm')")
> 
> pd = packLegend(lgd1, lgd2, lgd1, lgd2, lgd1, lgd2, max_height = unit(10, "cm"), gap = unit(1, "cm"))
> draw(pd, test = "many legends, max_height = unit(10, 'cm'), with gap")
> 
> lgd_long = Legend(at = 1:50, legend_gp = gpar(fill = 1:50))
> pd = packLegend(lgd1, lgd2, lgd1, lgd2, lgd1, lgd2, lgd_long, max_height = unit(10, "cm"))
> draw(pd, test = "many legends with a long one, max_height = unit(10, 'cm')")
> 
> lgd1 = Legend(at = 1:6, legend_gp = gpar(fill = 1:6), title = "legend1",
+ 	nr = 1)
> lgd2 = Legend(col_fun = col_fun, title = "legend2", at = c(0, 0.25, 0.5, 0.75, 1),
+ 	direction = "horizontal")
> pd = packLegend(lgd1, lgd2, lgd1, lgd2, lgd1, lgd2, direction = "horizontal")
> draw(pd, test = "many legends")
> 
> pd = packLegend(lgd1, lgd2, lgd1, lgd2, lgd1, lgd2, max_width = unit(1, "npc"), direction = "horizontal")
> draw(pd, test = "many legends, max_width = unit(1, 'npc')")
> ## reduce the height of the interactive window and rerun draw()
> 
> pd = packLegend(lgd1, lgd2, lgd1, lgd2, lgd1, lgd2, max_width = unit(10, "cm"), direction = "horizontal")
> draw(pd, test = "many legends, max_width = unit(10, 'cm')")
> 
> 
> ####### unequal interval breaks
> col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.1, 0.15, 0.5, 0.9, 0.95, 1))
> draw(lgd, test = "unequal interval breaks")
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.3, 1), legend_height = unit(4, "cm"))
> draw(lgd, test = "unequal interval breaks but not label position adjustment")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.1, 0.15, 0.5, 0.9, 0.95, 1),
+ 	direction = "horizontal")
> draw(lgd, test = "unequal interval breaks")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.1, 0.15, 0.5, 0.9, 0.95, 1),
+ 	direction = "horizontal", title_position = "lefttop")
> draw(lgd, test = "unequal interval breaks")
> 
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.1, 0.15, 0.5, 0.9, 0.95, 1),
+ 	direction = "horizontal", title_position = "lefttop", labels_rot = 90)
> draw(lgd, test = "unequal interval breaks, label rot 90")
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.1, 0.5, 0.75, 1),
+ 	labels = c("mininal", "q10", "median", "q75", "maximal"),
+ 	direction = "horizontal", title_position = "lefttop")
> draw(lgd, test = "unequal interval breaks with labels")
> 
> 
> lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.1, 0.5, 0.75, 1),
+ 	labels = c("mininal", "q10", "median", "q75", "maximal"),
+ 	direction = "horizontal")
> draw(lgd, test = "unequal interval breaks with labels")
> 
> 
> col_fun = colorRamp2(c(0, 0.05, 0.1, 0.5, 1), c("green", "white", "red", "black", "blue"))
> lgd = Legend(col_fun = col_fun, title = "foo", break_dist = 1:4)
> draw(lgd, test = "unequal interval breaks")
> 
> 
> #### position of legends to heatmaps ##
> if(0) {
+ m = matrix(rnorm(100), 10)
+ rownames(m) = random_str(10, len = 20)
+ colnames(m) = random_str(10, len = 20)
+ Heatmap(m)
+ }
> 
> 
> 
> proc.time()
   user  system elapsed 
   3.06    0.34    3.39 

ComplexHeatmap.Rcheck/tests/test-multiple-page.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> m = matrix(rnorm(100), 10)
> 
> postscript("test.ps")
> lgd = Legend(labels = c("a", "b", "c"))
> draw(Heatmap(m), heatmap_legend_list = list(lgd))
> dev.off()
null device 
          1 
> 
> check_pages = function() {
+ 	lines = readLines("test.ps")
+ 	print(lines[length(lines)-1])
+ 	invisible(file.remove("test.ps"))
+ }
> 
> check_pages()
[1] "%%Pages: 1"
> 
> postscript("test.ps")
> ha = HeatmapAnnotation(foo = 1:10, bar = anno_points(1:10))
> Heatmap(m, top_annotation = ha)
> dev.off()
null device 
          1 
> 
> check_pages()
[1] "%%Pages: 1"
> 
> proc.time()
   user  system elapsed 
   5.46    0.57    5.57 

ComplexHeatmap.Rcheck/tests/test-oncoPrint.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> mat = read.table(textConnection(
+ "s1,s2,s3
+ g1,snv;indel,snv,indel
+ g2,,snv;indel,snv
+ g3,snv,,indel;snv"), row.names = 1, header = TRUE, sep = ",", stringsAsFactors = FALSE)
> mat = as.matrix(mat)
> 
> get_type_fun = function(x) strsplit(x, ";")[[1]]
> 
> alter_fun = list(
+     snv = function(x, y, w, h) grid.rect(x, y, w*0.9, h*0.9, 
+         gp = gpar(fill = col["snv"], col = NA)),
+     indel = function(x, y, w, h) grid.rect(x, y, w*0.9, h*0.4, 
+         gp = gpar(fill = col["indel"], col = NA))
+ )
> 
> col = c(snv = "red", indel = "blue")
> ht = oncoPrint(mat, get_type = get_type_fun,
+     alter_fun = alter_fun, col = col)
All mutation types: snv, indel.
`alter_fun` is assumed vectorizable. If it does not generate correct
plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
> draw(ht)
> 
> ## turn off row names while turn on column names
> ht = oncoPrint(mat, get_type = get_type_fun,
+     alter_fun = alter_fun, col = col, 
+     show_column_names = TRUE, show_row_names = FALSE, show_pct = FALSE)
All mutation types: snv, indel.
`alter_fun` is assumed vectorizable. If it does not generate correct
plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
> draw(ht)
> 
> ht = oncoPrint(mat, get_type = get_type_fun,
+     alter_fun = alter_fun, col = col, pct_side = "right", 
+     row_names_side = "left")
All mutation types: snv, indel.
`alter_fun` is assumed vectorizable. If it does not generate correct
plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
> draw(ht)
> 
> ht = oncoPrint(mat, get_type = get_type_fun,
+     alter_fun = alter_fun, col = col,
+     top_annotation = HeatmapAnnotation(column_barplot = anno_oncoprint_barplot())
+ )
All mutation types: snv, indel.
`alter_fun` is assumed vectorizable. If it does not generate correct
plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
> draw(ht)
> 
> ht = oncoPrint(mat, get_type = get_type_fun,
+     alter_fun = alter_fun, col = col,
+     top_annotation = HeatmapAnnotation(
+     	column_barplot = anno_oncoprint_barplot(),
+     	foo = 1:3,
+     	annotation_name_side = "left")
+ )
All mutation types: snv, indel.
`alter_fun` is assumed vectorizable. If it does not generate correct
plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
> draw(ht)
> 
> ht = oncoPrint(mat, get_type = get_type_fun,
+     alter_fun = alter_fun, col = col,
+     top_annotation = HeatmapAnnotation(
+     	cbar = anno_oncoprint_barplot(),
+     	foo1 = 1:3,
+     	annotation_name_side = "left"),
+     left_annotation = rowAnnotation(foo2 = 1:3),
+     right_annotation = rowAnnotation(cbar = anno_oncoprint_barplot(), foo3 = 1:3),
+ )
All mutation types: snv, indel.
`alter_fun` is assumed vectorizable. If it does not generate correct
plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
> draw(ht)
> 
> 
> ht = oncoPrint(mat, get_type = get_type_fun,
+     alter_fun = alter_fun, col = col,
+     top_annotation = HeatmapAnnotation(
+         cbar = anno_oncoprint_barplot(border = TRUE),
+         foo1 = 1:3,
+         annotation_name_side = "left"),
+     left_annotation = rowAnnotation(foo2 = 1:3),
+     right_annotation = rowAnnotation(
+         cbar = anno_oncoprint_barplot(border = TRUE), 
+         foo3 = 1:3),
+ )
All mutation types: snv, indel.
`alter_fun` is assumed vectorizable. If it does not generate correct
plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
> draw(ht)
> 
> ht = oncoPrint(mat, get_type = get_type_fun,
+     alter_fun = alter_fun, col = col,
+     right_annotation = rowAnnotation(rbar = anno_oncoprint_barplot(axis_param = list(side = "bottom", labels_rot = 90)))
+ )
All mutation types: snv, indel.
`alter_fun` is assumed vectorizable. If it does not generate correct
plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
> draw(ht)
> 
> 
> proc.time()
   user  system elapsed 
   6.90    0.59    7.03 

ComplexHeatmap.Rcheck/tests/test-pheatmap.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> 
> if(requireNamespace("pheatmap")) {
+ 	mat = matrix(rnorm(100), 10)
+ 
+ 	compare_pheatmap(mat)
+ 
+ 	pheatmap(mat)
+ 	pheatmap(mat, col = rev(RColorBrewer::brewer.pal(n = 7, name = "RdYlBu")))
+ 
+ 	test = matrix(rnorm(200), 20, 10)
+ 	test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
+ 	test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
+ 	test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
+ 	colnames(test) = paste("Test", 1:10, sep = "")
+ 	rownames(test) = paste("Gene", 1:20, sep = "")
+ 
+ 	# Draw heatmaps
+ 	compare_pheatmap(test)
+ 	compare_pheatmap(test, kmeans_k = 2)
+ 	compare_pheatmap(test, scale = "row", clustering_distance_rows = "correlation")
+ 	compare_pheatmap(test, color = colorRampPalette(c("navy", "white", "firebrick3"))(50))
+ 	compare_pheatmap(test, cluster_row = FALSE)
+ 	compare_pheatmap(test, legend = FALSE)
+ 
+ 	# Show text within cells
+ 	compare_pheatmap(test, display_numbers = TRUE)
+ 	compare_pheatmap(test, display_numbers = TRUE, number_format = "%.1e")
+ 	compare_pheatmap(test, display_numbers = matrix(ifelse(test > 5, "*", ""), nrow(test)))
+ 	compare_pheatmap(test, cluster_row = FALSE, legend_breaks = -1:4, legend_labels = c("0",
+ 		"1e-4", "1e-3", "1e-2", "1e-1", "1"))
+ 
+ 	# Fix cell sizes and save to file with correct size
+ 	compare_pheatmap(test, cellwidth = 15, cellheight = 12, main = "Example heatmap")
+ 
+ 	# Generate annotations for rows and columns
+ 	annotation_col = data.frame(
+ 	    CellType = factor(rep(c("CT1", "CT2"), 5)), 
+ 	    Time = 1:5
+ 	)
+ 	rownames(annotation_col) = paste("Test", 1:10, sep = "")
+ 
+ 	annotation_row = data.frame(
+ 	    GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6)))
+ 	)
+ 	rownames(annotation_row) = paste("Gene", 1:20, sep = "")
+ 
+ 	# Display row and color annotations
+ 	compare_pheatmap(test, annotation_col = annotation_col)
+ 	compare_pheatmap(test, annotation_col = annotation_col, annotation_legend = FALSE)
+ 	compare_pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row)
+ 
+ 	# Change angle of text in the columns
+ 	compare_pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row, angle_col = "45")
+ 	compare_pheatmap(test, annotation_col = annotation_col, angle_col = "0")
+ 
+ 	# Specify colors
+ 	ann_colors = list(
+ 	    Time = c("white", "firebrick"),
+ 	    CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
+ 	    GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E")
+ 	)
+ 
+ 	compare_pheatmap(test, annotation_col = annotation_col, annotation_colors = ann_colors, main = "Title")
+ 	compare_pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row, 
+ 	         annotation_colors = ann_colors)
+ 	compare_pheatmap(test, annotation_col = annotation_col, annotation_colors = ann_colors[2]) 
+ 
+ 	# Gaps in heatmaps
+ 	compare_pheatmap(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14))
+ 	compare_pheatmap(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14), 
+ 	         cutree_col = 2)
+ 
+ 	# Show custom strings as row/col names
+ 	labels_row = c("", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
+ 		"", "", "Il10", "Il15", "Il1b")
+ 
+ 	compare_pheatmap(test, annotation_col = annotation_col, labels_row = labels_row)
+ 
+ 	# Specifying clustering from distance matrix
+ 	drows = dist(test, method = "minkowski")
+ 	dcols = dist(t(test), method = "minkowski")
+ 	compare_pheatmap(test, clustering_distance_rows = drows, clustering_distance_cols = dcols)
+ 
+ 	library(dendsort)
+ 
+ 	callback = function(hc, ...){dendsort(hc)}
+ 	compare_pheatmap(test, clustering_callback = callback)
+ }
Loading required namespace: pheatmap
Warning message:
argument `kmeans_k` is not suggested to use in pheatmap -> Heatmap
translation because it changes the input matrix. You might check
`row_km` and `column_km` arguments in Heatmap(). 
> 
> 
> set.seed(42)
> nsamples <- 10
> 
> mat <- matrix(rpois(20*nsamples, 20), ncol=nsamples)
> colnames(mat) <- paste0("sample", seq_len(ncol(mat)))
> rownames(mat) <- paste0("gene", seq_len(nrow(mat)))
> 
> annot <- data.frame(
+   labs = sample(c("A","B","C","D"), size = ncol(mat), replace = TRUE),
+   row.names = colnames(mat)
+ )
> ins <- list(mat = mat, annotation_col = annot)
> do.call(ComplexHeatmap::pheatmap, ins[1])
> do.call(ComplexHeatmap::pheatmap, ins)
> 
> proc.time()
   user  system elapsed 
  20.35    1.15   21.15 

ComplexHeatmap.Rcheck/tests/test-SingleAnnotation.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> ha = SingleAnnotation(value = 1:10)
> draw(ha, test = "single column annotation")
> ha = SingleAnnotation(value = 1:10, which = "row")
> draw(ha, test = "single row annotation")
> ha = SingleAnnotation(value = 1:10)
> draw(ha, index = 6:10, test = "single column annotation, subset")
> draw(ha, index = 6:10, k = 1, n = 2, test = "single column annotation, subset, k=1 n=2")
> draw(ha, index = 6:10, k = 2, n = 2, test = "single column annotation, subset, k=1 n=2")
> 
> x = 1:10
> ha = SingleAnnotation(value = x)
> draw(ha, test = "single column annotation")
> 
> m = cbind(1:10, 10:1)
> colnames(m) = c("a", "b")
> ha = SingleAnnotation(value = m)
> draw(ha, test = "matrix as column annotation")
> 
> ha = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))
> draw(ha, test = "color mapping function")
> 
> ha = SingleAnnotation(value = c(rep(c("a", "b"), 5)))
> draw(ha, test = "discrete annotation")
> ha = SingleAnnotation(value = c(rep(c("a", "b"), 5)), col = c("a" = "red", "b" = "blue"))
> draw(ha, test = "discrete annotation with defined colors")
> 
> anno = anno_simple(1:10)
> ha = SingleAnnotation(fun = anno)
> draw(ha, test = "AnnotationFunction as input")
> 
> anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)))
> ha = SingleAnnotation(fun = anno)
> draw(ha, test = "anno_barplot as input")
> draw(ha, index = 1:5, test = "anno_barplot as input, 1:5")
> draw(ha, index = 1:5, k = 1, n = 2, test = "anno_barplot as input, 1:5, k = 1, n = 2")
> draw(ha, index = 1:5, k = 2, n = 2, test = "anno_barplot as input, 1:5, k = 2, n = 2")
> 
> lt = lapply(1:20, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
> anno = anno_horizon(lt, which = "row")
> ha = SingleAnnotation(fun = anno, which = "row")
> draw(ha, test = "anno_horizon as input")
> 
> fun = local({
+ 	value = 1:10
+ 	function(index, k = 1, n = 1) {
+ 		pushViewport(viewport(xscale = c(0.5, length(index) + 0.5), yscale = range(value)))
+ 		grid.points(seq_along(index), value[index])
+ 		grid.rect()
+ 		if(k == 1) grid.yaxis()
+ 		popViewport()
+ 	}
+ })
> ha = SingleAnnotation(fun = fun, height = unit(4, "cm"))
> # ha[1:5]
> draw(ha, index = c(1, 4, 2, 6), test = "self-defined function")
> draw(ha, index = c(1, 4, 2, 6), k = 1, n = 2, test = "self-defined function, k = 1, n = 2")
> draw(ha, index = c(1, 4, 2, 6), k = 2, n = 2, test = "self-defined function, k = 2, n = 2")
> 
> 
> # test gridtext
> ha = SingleAnnotation(value = 1:10, label = gt_render("foo", r = unit(2, "pt")), name_gp = gpar(box_fill = "red"))
Loading required namespace: gridtext
> draw(ha, test = "single column annotation")
> 
> 
> 
> proc.time()
   user  system elapsed 
   3.35    0.34    3.65 

ComplexHeatmap.Rcheck/tests/test-textbox.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> 
> words = sapply(1:30, function(x) strrep(sample(letters, 1), sample(3:10, 1)))
> grid.newpage()
> grid.textbox(words, gp = gpar(fontsize = runif(30, min = 5, max = 30)))
> 
> sentenses = c("This is sentense 1", "This is a long long long long long long long sentense.")
> grid.newpage()
> grid.textbox(sentenses)
> grid.textbox(sentenses, word_wrap = TRUE)
> grid.textbox(sentenses, word_wrap = TRUE, add_new_line = TRUE)
> 
> 
> require(circlize)
Loading required package: circlize
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> mat = matrix(rnorm(100*10), nrow = 100)
> 
> split = sample(letters[1:10], 100, replace = TRUE)
> text = lapply(unique(split), function(x) {
+ 	data.frame(month.name, col = rand_color(12, friendly = TRUE), fontsize = runif(12, 6, 14))
+ })
> names(text) = unique(split)
> 
> Heatmap(mat, cluster_rows = FALSE, row_split = split,
+     right_annotation = rowAnnotation(wc = anno_textbox(split, text))
+ )
> 
> proc.time()
   user  system elapsed 
   3.32    0.60    3.39 

ComplexHeatmap.Rcheck/tests/test-upset.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> set.seed(123)
> lt = list(a = sample(letters, 10),
+ 	      b = sample(letters, 15),
+ 	      c = sample(letters, 20))
> 
> m = make_comb_mat(lt)
> t(m)
A combination matrix with 3 sets and 6 combinations.
  ranges of combination set size: c(1, 8).
  mode for the combination size: distinct.
  sets are on columns

Combination sets are:
  a b c code size
  x x x  111    4
  x x    110    4
  x   x  101    2
    x x  011    6
    x    010    1
      x  001    8

Sets are:
  set size
    a   10
    b   15
    c   20
> set_name(m)
[1] "a" "b" "c"
> comb_name(m)
[1] "111" "110" "101" "011" "010" "001"
> set_size(m)
 a  b  c 
10 15 20 
> comb_size(m)
111 110 101 011 010 001 
  4   4   2   6   1   8 
> lapply(comb_name(m), function(x) extract_comb(m, x))
[[1]]
[1] "e" "j" "x" "y"

[[2]]
[1] "c" "k" "n" "s"

[[3]]
[1] "o" "r"

[[4]]
[1] "a" "g" "h" "i" "l" "u"

[[5]]
[1] "d"

[[6]]
[1] "b" "f" "m" "q" "t" "v" "w" "z"

> draw(UpSet(m))
> draw(UpSet(m, comb_col = c(rep(2, 3), rep(3, 3), 1)))
> draw(UpSet(t(m)))
> 
> set_name(t(m))
[1] "a" "b" "c"
> comb_name(t(m))
[1] "111" "110" "101" "011" "010" "001"
> set_size(t(m))
 a  b  c 
10 15 20 
> comb_size(t(m))
111 110 101 011 010 001 
  4   4   2   6   1   8 
> lapply(comb_name(t(m)), function(x) extract_comb(t(m), x))
[[1]]
[1] "e" "j" "x" "y"

[[2]]
[1] "c" "k" "n" "s"

[[3]]
[1] "o" "r"

[[4]]
[1] "a" "g" "h" "i" "l" "u"

[[5]]
[1] "d"

[[6]]
[1] "b" "f" "m" "q" "t" "v" "w" "z"

> 
> m = make_comb_mat(lt, mode = "intersect")
> lapply(comb_name(m), function(x) extract_comb(m, x))
[[1]]
[1] "e" "j" "x" "y"

[[2]]
[1] "c" "e" "j" "k" "n" "s" "x" "y"

[[3]]
[1] "e" "j" "o" "r" "x" "y"

[[4]]
 [1] "a" "e" "g" "h" "i" "j" "l" "u" "x" "y"

[[5]]
 [1] "c" "e" "j" "k" "n" "o" "r" "s" "x" "y"

[[6]]
 [1] "a" "c" "d" "e" "g" "h" "i" "j" "k" "l" "n" "s" "u" "x" "y"

[[7]]
 [1] "a" "b" "e" "f" "g" "h" "i" "j" "l" "m" "o" "q" "r" "t" "u" "v" "w" "x" "y"
[20] "z"

> draw(UpSet(m))
> 
> m = make_comb_mat(lt, mode = "union")
> lapply(comb_name(m), function(x) extract_comb(m, x))
[[1]]
 [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "q" "r" "s" "t"
[20] "u" "v" "w" "x" "y" "z"

[[2]]
 [1] "a" "c" "d" "e" "g" "h" "i" "j" "k" "l" "n" "o" "r" "s" "u" "x" "y"

[[3]]
 [1] "a" "b" "c" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "q" "r" "s" "t" "u"
[20] "v" "w" "x" "y" "z"

[[4]]
 [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "q" "r" "s" "t"
[20] "u" "v" "w" "x" "y" "z"

[[5]]
 [1] "c" "e" "j" "k" "n" "o" "r" "s" "x" "y"

[[6]]
 [1] "a" "c" "d" "e" "g" "h" "i" "j" "k" "l" "n" "s" "u" "x" "y"

[[7]]
 [1] "a" "b" "e" "f" "g" "h" "i" "j" "l" "m" "o" "q" "r" "t" "u" "v" "w" "x" "y"
[20] "z"

> draw(UpSet(m))
> 
> f = system.file("extdata", "movies.csv", package = "UpSetR")
> if(file.exists(f)) {
+ 	movies <- read.csv(system.file("extdata", "movies.csv", package = "UpSetR"), header = T, sep = ";")
+ 	m = make_comb_mat(movies, top_n_sets = 6)
+ 	t(m)
+ 	set_name(m)
+ 	comb_name(m)
+ 	set_size(m)
+ 	comb_size(m)
+ 	lapply(comb_name(m), function(x) extract_comb(m, x))
+ 
+ 	set_name(t(m))
+ 	comb_name(t(m))
+ 	set_size(t(m))
+ 	comb_size(t(m))
+ 	lapply(comb_name(t(m)), function(x) extract_comb(t(m), x))
+ 
+ 	draw(UpSet(m))
+ 	draw(UpSet(t(m)))
+ 
+ 	m = make_comb_mat(movies, top_n_sets = 6, mode = "intersect")
+ 	m = make_comb_mat(movies, top_n_sets = 6, mode = "union")
+ }
> 
> library(circlize)
> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> lt = lapply(1:4, function(i) generateRandomBed())
> lt = lapply(lt, function(df) GRanges(seqnames = df[, 1], ranges = IRanges(df[, 2], df[, 3])))
> names(lt) = letters[1:4]
> m = make_comb_mat(lt)
> 
> # if(0) {
> # set.seed(123)
> # lt = list(a = sample(letters, 10),
> # 	      b = sample(letters, 15),
> # 	      c = sample(letters, 20))
> # v = gplots::venn(lt, show.plot = FALSE)
> # rownames(v) = apply(v[, -1], 1, paste, collapse = "")
> # m = make_comb_mat(lt)
> # cs = structure(comb_size(m), names = comb_name(m))
> # }
> 
> if(file.exists(f)) {
+ 	movies <- read.csv(f, header = T, sep = ";")
+ 	genre = c("Action", "Romance", "Horror", "Children", "SciFi", "Documentary")
+ 	rate = cut(movies$AvgRating, c(0, 1, 2, 3, 4, 5))
+ 	m_list = tapply(seq_len(nrow(movies)), rate, function(ind) {
+ 		make_comb_mat(movies[ind, genre, drop = FALSE])
+ 	})
+ 	m_list2 = normalize_comb_mat(m_list)
+ 
+ 	lapply(m_list2, set_name)
+ 	lapply(m_list2, set_size)
+ 	lapply(m_list2, comb_name)
+ 	lapply(m_list2, comb_size)
+ 
+ 	lapply(1:length(m_list), function(i) {
+ 		n1 = comb_name(m_list[[i]])
+ 		x1 = comb_size(m_list[[i]])
+ 		n2 = comb_name(m_list2[[i]])
+ 		x2 = comb_size(m_list2[[i]])
+ 		l = n2 %in% n1
+ 		x2[!l]
+ 	})
+ }
[[1]]
110001 100101 100011 110000 100100 100010 100001 010100 010010 010001 000110 
     0      0      0      0      0      0      0      0      0      0      0 
000101 000011 100000 000010 
     0      0      0      1 

[[2]]
110001 100101 100011 100001 010100 010010 010001 000110 000101 000011 
     1      1      0      5      0      0      0      0      8      0 

[[3]]
110001 100101 100011 100001 010001 000101 000011 
     0      4      0     35      7     27      1 

[[4]]
110001 100101 100011 100100 100001 010001 000101 000011 
     1      6      1      6     45      5     11      4 

[[5]]
110001 100101 100011 100100 100001 010100 010010 010001 000110 000101 000011 
     0      1      1      1      6      0      0      0      0      0      0 

> 
> 
> proc.time()
   user  system elapsed 
  14.28    0.90   14.76 

ComplexHeatmap.Rcheck/tests/test-utils.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(circlize)
========================================
circlize version 0.4.16
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> library(GetoptLong)
> 
> # things needed to be tested
> # 1. the order
> # 2. if the sum of sizes are larger than xlim
> 
> make_plot = function(pos1, pos2, range) {
+ 	oxpd = par("xpd")
+ 	par(xpd = NA)
+ 	plot(NULL, xlim = c(0, 4), ylim = range, ann = FALSE)
+ 	col = rand_color(nrow(pos1), transparency = 0.5)
+ 	rect(0.5, pos1[, 1], 1.5, pos1[, 2], col = col)
+ 	rect(2.5, pos2[, 1], 3.5, pos2[, 2], col = col)
+ 	segments(1.5, rowMeans(pos1), 2.5, rowMeans(pos2))
+ 	par(xpd = oxpd)
+ }
> 
> range = c(0, 10)
> pos1 = rbind(c(1, 2), c(5, 7))
> make_plot(pos1, smartAlign2(pos1, range = range), range)
> 
> range = c(0, 10)
> pos1 = rbind(c(-0.5, 2), c(5, 7))
> make_plot(pos1, smartAlign2(pos1, range = range), range)
> 
> pos1 = rbind(c(-1, 2), c(3, 4), c(5, 6), c(7, 11))
> pos1 = pos1 + runif(length(pos1), max = 0.3, min = -0.3)
> par(mfrow = c(3, 3))
> for(i in 1:9) {
+ 	ind = sample(4, 4)
+ 	make_plot(pos1[ind, ], smartAlign2(pos1[ind, ], range = range), range)
+ }
> par(mfrow = c(1, 1))
> 
> pos1 = rbind(c(3, 6), c(4, 7))
> make_plot(pos1, smartAlign2(pos1, range = range), range)
> 
> pos1 = rbind(c(1, 8), c(3, 10))
> make_plot(pos1, smartAlign2(pos1, range = range), range)
> 
> ########## new version of smartAlign2() ############
> 
> start = c(0.0400972528391016, 0.0491583597430212, 0.0424302664385027, 0.0547524243812509, 0.0820937279769642, 0.126861283282835, 0.178503822565168, 0.327742831447437, 0.570671411156898, 0.81775868755151)
> end = c(0.0921142856224367, 0.107091640256979, 0.137858195099959, 0.159189883311057, 0.177521656638421, 0.20727333210178, 0.304669254357909, 0.463122553167947, 0.676924742689255, 0.929837466294643)
> range = c(0, 1)
> smartAlign2(start, end, range, plot = TRUE)
enter to continue
             [,1]       [,2]
 [1,] 0.002200888 0.05421792
 [2,] 0.054217921 0.11215120
 [3,] 0.112151202 0.20757913
 [4,] 0.207579130 0.31201659
 [5,] 0.312016589 0.40744452
 [6,] 0.407444518 0.48785657
 [7,] 0.487856567 0.61402200
 [8,] 0.614021999 0.74940172
 [9,] 0.749401720 0.85565505
[10,] 0.855655052 0.96773383
> 
> 
> start <- c(0.722121284290678, 0.701851666769472, 0.284795592003117, 0.335674695572052, 0.246977082249377, 0.767289857630785, 0.728198060058033, 0.299241440370817, -0.0149946764559372, 0.85294351791166, 0.126216621670218, 0.478169948493225)
> end <- c(0.766196472718668, 0.763101604258565, 0.34604552949221, 0.421334650222341, 0.344144413077725, 0.847196123677626, 0.813858014708322, 0.392347344675911, 0.108452620381171, 0.969486388630396, 0.249951602628847, 0.584914163656308)
> od = order(start)
> start = start[od]; end = end[od]
> range = c(0, 1)
> pos = smartAlign2(start, end, range)
> n = nrow(pos)
> pos[1:(n-1), 2] > pos[2:n, 1]
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> 
> 
> if(0) {
+ 	go_id = random_GO(500)
+ 	mat = GO_similarity(go_id)
+ 	invisible(simplify(mat, order_by_size = FALSE))
+ }
> 
> proc.time()
   user  system elapsed 
   2.01    0.25    2.21 

ComplexHeatmap.Rcheck/tests/testthat-all.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> 
> suppressWarnings(suppressPackageStartupMessages(library(ComplexHeatmap)))
> library(testthat)
> 
> test_check("ComplexHeatmap")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
  19.75    0.84   27.29 

Example timings

ComplexHeatmap.Rcheck/ComplexHeatmap-Ex.timings

nameusersystemelapsed
AdditiveUnit-class000
AdditiveUnit000
AnnotationFunction-class000
AnnotationFunction3.560.443.53
ColorMapping-class000
ColorMapping0.010.000.02
ComplexHeatmap-package000
Extract.AnnotationFunction0.030.000.03
Extract.Heatmap0.440.000.44
Extract.HeatmapAnnotation0.030.000.03
Extract.HeatmapList0.110.000.11
Extract.SingleAnnotation0.000.010.00
Extract.comb_mat0.020.000.01
Extract.gridtext000
Heatmap-class000
Heatmap000
Heatmap3D0.120.000.13
HeatmapAnnotation-class000
HeatmapAnnotation000
HeatmapList-class000
HeatmapList000
Legend0.060.000.07
Legends-class0.010.000.01
Legends000
SingleAnnotation-class000
SingleAnnotation0.050.020.06
UpSet0.410.010.44
add.AdditiveUnit000
add_heatmap-Heatmap-method000
add_heatmap-HeatmapAnnotation-method000
add_heatmap-HeatmapList-method000
add_heatmap-dispatch000
adjust_dend_by_x0.010.000.02
adjust_heatmap_list-HeatmapList-method000
alter_graphic0.140.000.14
anno_barplot0.020.000.01
anno_block0.810.000.82
anno_boxplot0.020.000.02
anno_customize0.540.010.56
anno_density0.470.020.48
anno_empty000
anno_histogram0.070.000.07
anno_horizon3.920.053.97
anno_image000
anno_joyplot0.340.040.39
anno_lines0.060.020.07
anno_link000
anno_mark0.390.010.41
anno_numeric0.140.020.16
anno_oncoprint_barplot000
anno_points0.020.000.01
anno_simple0.050.000.07
anno_summary0.250.000.25
anno_text0.070.000.06
anno_textbox0.510.000.52
anno_zoom0.280.020.30
annotation_axis_grob0.060.000.06
annotation_legend_size-HeatmapList-method000
attach_annotation-Heatmap-method0.490.000.48
bar3D0.010.000.02
bin_genome000
c.ColorMapping000
c.HeatmapAnnotation0.040.000.03
cluster_between_groups0.010.000.02
cluster_within_group0.030.000.03
color_mapping_legend-ColorMapping-method000
columnAnnotation000
column_dend-Heatmap-method0.270.000.26
column_dend-HeatmapList-method0.840.030.88
column_dend-dispatch000
column_order-Heatmap-method0.220.010.23
column_order-HeatmapList-method0.860.020.88
column_order-dispatch000
comb_degree0.020.000.01
comb_name000
comb_size000
compare_heatmap.20.790.060.88
compare_heatmap0.670.000.67
compare_pheatmap1.100.031.12
complement_size0.000.020.00
component_height-Heatmap-method000
component_height-HeatmapList-method000
component_height-dispatch000
component_width-Heatmap-method000
component_width-HeatmapList-method000
component_width-dispatch000
copy_all-AnnotationFunction-method000
copy_all-SingleAnnotation-method000
copy_all-dispatch000
decorate_annotation0.200.010.22
decorate_column_dend000
decorate_column_names000
decorate_column_title000
decorate_dend0.130.000.12
decorate_dimnames0.140.000.14
decorate_heatmap_body0.080.020.09
decorate_row_dend000
decorate_row_names000
decorate_row_title000
decorate_title0.130.000.13
default_axis_param000
default_get_type000
dend_heights000
dend_xy000
dendrogramGrob000
densityHeatmap0.920.010.94
dim.Heatmap000
dist2000
draw-AnnotationFunction-method000
draw-Heatmap-method000
draw-HeatmapAnnotation-method000
draw-HeatmapList-method000
draw-Legends-method0.020.000.02
draw-SingleAnnotation-method000
draw-dispatch000
draw_annotation-Heatmap-method000
draw_annotation_legend-HeatmapList-method000
draw_dend-Heatmap-method000
draw_dimnames-Heatmap-method000
draw_heatmap_body-Heatmap-method000
draw_heatmap_legend-HeatmapList-method000
draw_heatmap_list-HeatmapList-method000
draw_title-Heatmap-method000
draw_title-HeatmapList-method000
draw_title-dispatch000
extract_comb000
frequencyHeatmap0.360.040.39
full_comb_code000
getXY_in_parent_vp0.010.000.02
get_color_mapping_list-HeatmapAnnotation-method000
get_legend_param_list-HeatmapAnnotation-method000
grid.annotation_axis000
grid.boxplot000
grid.dendrogram0.280.040.33
grid.draw.Legends000
grid.textbox000
gt_render0.800.030.83
heatmap_legend_size-HeatmapList-method000
height.AnnotationFunction000
height.Heatmap000
height.HeatmapAnnotation000
height.HeatmapList000
height.Legends0.020.000.01
height.SingleAnnotation000
heightAssign.AnnotationFunction000
heightAssign.HeatmapAnnotation000
heightAssign.SingleAnnotation000
heightDetails.annotation_axis000
heightDetails.legend000
heightDetails.legend_body000
heightDetails.packed_legends000
heightDetails.textbox000
ht_global_opt000
ht_opt0.020.000.02
ht_size000
is_abs_unit000
length.HeatmapAnnotation000
length.HeatmapList000
list_components000
list_to_matrix000
make_column_cluster-Heatmap-method000
make_comb_mat0.000.020.01
make_layout-Heatmap-method000
make_layout-HeatmapList-method000
make_layout-dispatch000
make_row_cluster-Heatmap-method000
map_to_colors-ColorMapping-method0.010.000.02
max_text_height000
max_text_width000
merge_dendrogram0.080.000.08
names.HeatmapAnnotation0.020.000.01
names.HeatmapList000
namesAssign.HeatmapAnnotation0.010.000.02
ncol.Heatmap000
nobs.AnnotationFunction000
nobs.HeatmapAnnotation000
nobs.SingleAnnotation000
normalize_comb_mat000
normalize_genomic_signals_to_bins000
nrow.Heatmap000
oncoPrint000
order.comb_mat000
packLegend0.050.000.04
pct_v_pct000
pheatmap000
pindex000
plot.Heatmap000
plot.HeatmapAnnotation000
plot.HeatmapList000
prepare-Heatmap-method000
print.comb_mat000
re_size-HeatmapAnnotation-method000
restore_matrix0.320.000.31
rowAnnotation000
row_anno_barplot000
row_anno_boxplot000
row_anno_density000
row_anno_histogram000
row_anno_points000
row_anno_text000
row_dend-Heatmap-method0.250.000.25
row_dend-HeatmapList-method0.560.030.59
row_dend-dispatch000
row_order-Heatmap-method0.220.020.24
row_order-HeatmapList-method0.590.000.59
row_order-dispatch000
set_component_height-Heatmap-method000
set_component_width-Heatmap-method000
set_name000
set_nameAssign000
set_size000
show-AnnotationFunction-method000
show-ColorMapping-method000
show-Heatmap-method000
show-HeatmapAnnotation-method000
show-HeatmapList-method000
show-SingleAnnotation-method000
show-dispatch000
size.AnnotationFunction000
size.HeatmapAnnotation000
size.SingleAnnotation000
sizeAssign.AnnotationFunction000
sizeAssign.HeatmapAnnotation000
sizeAssign.SingleAnnotation000
smartAlign20.140.010.16
str.comb_mat000
subset_gp000
subset_matrix_by_row000
subset_no000
subset_vector000
summary.Heatmap000
summary.HeatmapList000
t.comb_mat000
test_alter_fun0.050.000.04
textbox_grob0.070.000.08
unify_mat_list000
upset_left_annotation000
upset_right_annotation000
upset_top_annotation000
width.AnnotationFunction000
width.Heatmap000
width.HeatmapAnnotation000
width.HeatmapList000
width.Legends0.020.000.01
width.SingleAnnotation000
widthAssign.AnnotationFunction000
widthAssign.HeatmapAnnotation000
widthAssign.SingleAnnotation000
widthDetails.annotation_axis000
widthDetails.legend000
widthDetails.legend_body000
widthDetails.packed_legends000
widthDetails.textbox000