Zuguang Gu
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ComplexHeatmap |
| git_branch: master |
| git_last_commit: e5e685f |
| git_last_commit_date: 2021-10-26 12:19:39 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:15 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the ComplexHeatmap package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 381/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ComplexHeatmap 2.11.0 (landing page) Zuguang Gu
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ComplexHeatmap |
| Version: 2.11.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ComplexHeatmap.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ComplexHeatmap_2.11.0.tar.gz |
| StartedAt: 2022-03-17 18:47:36 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:52:36 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 299.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ComplexHeatmap.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ComplexHeatmap.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ComplexHeatmap_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ComplexHeatmap.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ComplexHeatmap/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ComplexHeatmap' version '2.11.0' * 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 R 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 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-upset.R' Running 'test-utils.R' Running 'testthat-all.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
ComplexHeatmap.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ComplexHeatmap
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ComplexHeatmap' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ComplexHeatmap'
finding HTML links ... done
AdditiveUnit-class html
AdditiveUnit html
AnnotationFunction-class html
AnnotationFunction html
ColorMapping-class html
ColorMapping html
ComplexHeatmap-package html
Extract.AnnotationFunction html
Extract.Heatmap html
Extract.HeatmapAnnotation html
Extract.HeatmapList html
Extract.SingleAnnotation html
Extract.comb_mat html
Extract.gridtext html
Heatmap-class html
Heatmap html
Heatmap3D html
HeatmapAnnotation-class html
HeatmapAnnotation html
HeatmapList-class html
HeatmapList html
Legend html
Legends-class html
Legends html
SingleAnnotation-class html
SingleAnnotation html
UpSet html
add.AdditiveUnit html
add_heatmap-Heatmap-method html
add_heatmap-HeatmapAnnotation-method html
add_heatmap-HeatmapList-method html
add_heatmap-dispatch html
adjust_dend_by_x html
adjust_heatmap_list-HeatmapList-method
html
alter_graphic html
anno_barplot html
anno_block html
anno_boxplot html
anno_customize html
anno_density html
anno_empty html
anno_histogram html
anno_horizon html
anno_image html
anno_joyplot html
anno_lines html
anno_link html
anno_mark html
anno_oncoprint_barplot html
anno_points html
anno_simple html
anno_summary html
anno_text html
anno_zoom html
annotation_axis_grob html
annotation_legend_size-HeatmapList-method
html
attach_annotation-Heatmap-method html
bar3D html
bin_genome html
c.ColorMapping html
c.HeatmapAnnotation html
cluster_between_groups html
cluster_within_group html
color_mapping_legend-ColorMapping-method
html
columnAnnotation html
column_dend-Heatmap-method html
column_dend-HeatmapList-method html
column_dend-dispatch html
column_order-Heatmap-method html
column_order-HeatmapList-method html
column_order-dispatch html
comb_degree html
comb_name html
comb_size html
compare_heatmap.2 html
compare_heatmap html
compare_pheatmap html
complement_size html
component_height-Heatmap-method html
component_height-HeatmapList-method html
component_height-dispatch html
component_width-Heatmap-method html
component_width-HeatmapList-method html
component_width-dispatch html
copy_all-AnnotationFunction-method html
copy_all-SingleAnnotation-method html
copy_all-dispatch html
decorate_annotation html
decorate_column_dend html
decorate_column_names html
decorate_column_title html
decorate_dend html
decorate_dimnames html
decorate_heatmap_body html
decorate_row_dend html
decorate_row_names html
decorate_row_title html
decorate_title html
default_axis_param html
default_get_type html
dend_heights html
dend_xy html
dendrogramGrob html
densityHeatmap html
dim.Heatmap html
dist2 html
draw-AnnotationFunction-method html
draw-Heatmap-method html
draw-HeatmapAnnotation-method html
draw-HeatmapList-method html
draw-Legends-method html
draw-SingleAnnotation-method html
draw-dispatch html
draw_annotation-Heatmap-method html
draw_annotation_legend-HeatmapList-method
html
draw_dend-Heatmap-method html
draw_dimnames-Heatmap-method html
draw_heatmap_body-Heatmap-method html
draw_heatmap_legend-HeatmapList-method
html
draw_heatmap_list-HeatmapList-method html
draw_title-Heatmap-method html
draw_title-HeatmapList-method html
draw_title-dispatch html
extract_comb html
frequencyHeatmap html
full_comb_code html
getXY_in_parent_vp html
get_color_mapping_list-HeatmapAnnotation-method
html
get_legend_param_list-HeatmapAnnotation-method
html
grid.annotation_axis html
grid.boxplot html
grid.dendrogram html
grid.draw.Legends html
gt_render html
heatmap_legend_size-HeatmapList-method
html
height.AnnotationFunction html
height.Heatmap html
height.HeatmapAnnotation html
height.HeatmapList html
height.Legends html
height.SingleAnnotation html
heightAssign.AnnotationFunction html
heightAssign.HeatmapAnnotation html
heightAssign.SingleAnnotation html
heightDetails.annotation_axis html
heightDetails.legend html
heightDetails.legend_body html
heightDetails.packed_legends html
ht_global_opt html
ht_opt html
ht_size html
is_abs_unit html
length.HeatmapAnnotation html
length.HeatmapList html
list_components html
list_to_matrix html
make_column_cluster-Heatmap-method html
make_comb_mat html
make_layout-Heatmap-method html
make_layout-HeatmapList-method html
make_layout-dispatch html
make_row_cluster-Heatmap-method html
map_to_colors-ColorMapping-method html
max_text_height html
max_text_width html
merge_dendrogram html
names.HeatmapAnnotation html
names.HeatmapList html
namesAssign.HeatmapAnnotation html
ncol.Heatmap html
nobs.AnnotationFunction html
nobs.HeatmapAnnotation html
nobs.SingleAnnotation html
normalize_comb_mat html
normalize_genomic_signals_to_bins html
nrow.Heatmap html
oncoPrint html
order.comb_mat html
packLegend html
pct_v_pct html
pheatmap html
pindex html
plot.Heatmap html
plot.HeatmapAnnotation html
plot.HeatmapList html
prepare-Heatmap-method html
print.comb_mat html
re_size-HeatmapAnnotation-method html
restore_matrix html
rowAnnotation html
row_anno_barplot html
row_anno_boxplot html
row_anno_density html
row_anno_histogram html
row_anno_points html
row_anno_text html
row_dend-Heatmap-method html
row_dend-HeatmapList-method html
row_dend-dispatch html
row_order-Heatmap-method html
row_order-HeatmapList-method html
row_order-dispatch html
set_component_height-Heatmap-method html
set_component_width-Heatmap-method html
set_name html
set_nameAssign html
set_size html
show-AnnotationFunction-method html
show-ColorMapping-method html
show-Heatmap-method html
show-HeatmapAnnotation-method html
show-HeatmapList-method html
show-SingleAnnotation-method html
show-dispatch html
size.AnnotationFunction html
size.HeatmapAnnotation html
size.SingleAnnotation html
sizeAssign.AnnotationFunction html
sizeAssign.HeatmapAnnotation html
sizeAssign.SingleAnnotation html
smartAlign2 html
str.comb_mat html
subset_gp html
subset_matrix_by_row html
subset_no html
subset_vector html
summary.Heatmap html
summary.HeatmapList html
t.comb_mat html
test_alter_fun html
unify_mat_list html
upset_left_annotation html
upset_right_annotation html
upset_top_annotation html
width.AnnotationFunction html
width.Heatmap html
width.HeatmapAnnotation html
width.HeatmapList html
width.Legends html
width.SingleAnnotation html
widthAssign.AnnotationFunction html
widthAssign.HeatmapAnnotation html
widthAssign.SingleAnnotation html
widthDetails.annotation_axis html
widthDetails.legend html
widthDetails.legend_body html
widthDetails.packed_legends html
** 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)
Making 'packages.html' ... done
ComplexHeatmap.Rcheck/tests/test-annotation_axis.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 2.11.0
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:
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
2.12 0.26 2.34
ComplexHeatmap.Rcheck/tests/test-AnnotationFunction.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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_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_custome ###
> 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.
>
>
>
> proc.time()
user system elapsed
15.51 0.29 15.86
ComplexHeatmap.Rcheck/tests/test-ColorMapping-class.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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
1.70 0.21 1.90
ComplexHeatmap.Rcheck/tests/test-dendrogram.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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 1.15.2
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
5.46 0.54 6.01
ComplexHeatmap.Rcheck/tests/test-gridtext.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 2.11.0
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:
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
3.01 0.34 3.32
ComplexHeatmap.Rcheck/tests/test-Heatmap-class.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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 1.15.2
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
17.70 0.48 18.21
ComplexHeatmap.Rcheck/tests/test-Heatmap-cluster.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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
1.73 0.20 1.92
ComplexHeatmap.Rcheck/tests/test-HeatmapAnnotation.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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 subsetable
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 subsetable
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 subsetable
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)
>
> proc.time()
user system elapsed
9.09 0.37 9.45
ComplexHeatmap.Rcheck/tests/test-HeatmapList-class.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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
11.15 0.46 11.59
ComplexHeatmap.Rcheck/tests/test-interactive.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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
0.15 0.03 0.17
ComplexHeatmap.Rcheck/tests/test-Legend.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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
3.35 0.25 3.59
ComplexHeatmap.Rcheck/tests/test-multiple-page.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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
4.42 0.26 4.68
ComplexHeatmap.Rcheck/tests/test-oncoPrint.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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 0.4.14 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 2.11.0 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: 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 6.34 0.34 6.67
ComplexHeatmap.Rcheck/tests/test-pheatmap.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 2.11.0
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:
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
19.65 0.34 20.03
ComplexHeatmap.Rcheck/tests/test-SingleAnnotation.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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
3.26 0.26 3.51
ComplexHeatmap.Rcheck/tests/test-upset.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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, 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, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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
17.71 0.51 18.17
ComplexHeatmap.Rcheck/tests/test-utils.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 0.4.14
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 2.11.0
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:
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
1.70 0.25 1.93
ComplexHeatmap.Rcheck/tests/testthat-all.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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
22.75 0.60 32.42
ComplexHeatmap.Rcheck/ComplexHeatmap-Ex.timings
| name | user | system | elapsed | |
| AdditiveUnit-class | 0 | 0 | 0 | |
| AdditiveUnit | 0 | 0 | 0 | |
| AnnotationFunction-class | 0 | 0 | 0 | |
| AnnotationFunction | 2.89 | 0.17 | 3.06 | |
| ColorMapping-class | 0 | 0 | 0 | |
| ColorMapping | 0.01 | 0.00 | 0.02 | |
| ComplexHeatmap-package | 0 | 0 | 0 | |
| Extract.AnnotationFunction | 0.02 | 0.00 | 0.01 | |
| Extract.Heatmap | 0.34 | 0.01 | 0.36 | |
| Extract.HeatmapAnnotation | 0.03 | 0.00 | 0.03 | |
| Extract.HeatmapList | 0.10 | 0.00 | 0.09 | |
| Extract.SingleAnnotation | 0 | 0 | 0 | |
| Extract.comb_mat | 0.02 | 0.00 | 0.01 | |
| Extract.gridtext | 0 | 0 | 0 | |
| Heatmap-class | 0 | 0 | 0 | |
| Heatmap | 0 | 0 | 0 | |
| Heatmap3D | 0.11 | 0.00 | 0.11 | |
| HeatmapAnnotation-class | 0 | 0 | 0 | |
| HeatmapAnnotation | 0 | 0 | 0 | |
| HeatmapList-class | 0 | 0 | 0 | |
| HeatmapList | 0 | 0 | 0 | |
| Legend | 0.04 | 0.00 | 0.05 | |
| Legends-class | 0.02 | 0.00 | 0.02 | |
| Legends | 0 | 0 | 0 | |
| SingleAnnotation-class | 0 | 0 | 0 | |
| SingleAnnotation | 0.03 | 0.00 | 0.03 | |
| UpSet | 0.38 | 0.00 | 0.37 | |
| add.AdditiveUnit | 0 | 0 | 0 | |
| add_heatmap-Heatmap-method | 0 | 0 | 0 | |
| add_heatmap-HeatmapAnnotation-method | 0 | 0 | 0 | |
| add_heatmap-HeatmapList-method | 0 | 0 | 0 | |
| add_heatmap-dispatch | 0 | 0 | 0 | |
| adjust_dend_by_x | 0.01 | 0.00 | 0.02 | |
| adjust_heatmap_list-HeatmapList-method | 0 | 0 | 0 | |
| alter_graphic | 0.13 | 0.00 | 0.12 | |
| anno_barplot | 0.01 | 0.00 | 0.02 | |
| anno_block | 0.58 | 0.00 | 0.58 | |
| anno_boxplot | 0.02 | 0.00 | 0.02 | |
| anno_customize | 0.45 | 0.00 | 0.45 | |
| anno_density | 0.33 | 0.01 | 0.34 | |
| anno_empty | 0.01 | 0.00 | 0.02 | |
| anno_histogram | 0.07 | 0.00 | 0.06 | |
| anno_horizon | 4.11 | 0.05 | 4.16 | |
| anno_image | 0 | 0 | 0 | |
| anno_joyplot | 0.39 | 0.02 | 0.42 | |
| anno_lines | 0.07 | 0.01 | 0.09 | |
| anno_link | 0 | 0 | 0 | |
| anno_mark | 0.57 | 0.00 | 0.57 | |
| anno_oncoprint_barplot | 0 | 0 | 0 | |
| anno_points | 0.01 | 0.02 | 0.03 | |
| anno_simple | 0.05 | 0.01 | 0.06 | |
| anno_summary | 0.37 | 0.00 | 0.38 | |
| anno_text | 0.10 | 0.00 | 0.09 | |
| anno_zoom | 0.48 | 0.00 | 0.48 | |
| annotation_axis_grob | 0.08 | 0.00 | 0.08 | |
| annotation_legend_size-HeatmapList-method | 0 | 0 | 0 | |
| attach_annotation-Heatmap-method | 0.69 | 0.00 | 0.69 | |
| bar3D | 0.01 | 0.00 | 0.01 | |
| bin_genome | 0 | 0 | 0 | |
| c.ColorMapping | 0 | 0 | 0 | |
| c.HeatmapAnnotation | 0.05 | 0.00 | 0.05 | |
| cluster_between_groups | 0.03 | 0.00 | 0.03 | |
| cluster_within_group | 0.02 | 0.00 | 0.01 | |
| color_mapping_legend-ColorMapping-method | 0 | 0 | 0 | |
| columnAnnotation | 0 | 0 | 0 | |
| column_dend-Heatmap-method | 0.35 | 0.00 | 0.34 | |
| column_dend-HeatmapList-method | 0.89 | 0.00 | 0.89 | |
| column_dend-dispatch | 0 | 0 | 0 | |
| column_order-Heatmap-method | 0.19 | 0.01 | 0.20 | |
| column_order-HeatmapList-method | 0.70 | 0.02 | 0.72 | |
| column_order-dispatch | 0 | 0 | 0 | |
| comb_degree | 0 | 0 | 0 | |
| comb_name | 0 | 0 | 0 | |
| comb_size | 0 | 0 | 0 | |
| compare_heatmap.2 | 0.74 | 0.00 | 0.77 | |
| compare_heatmap | 0.54 | 0.00 | 0.54 | |
| compare_pheatmap | 0.43 | 0.06 | 0.49 | |
| complement_size | 0 | 0 | 0 | |
| component_height-Heatmap-method | 0 | 0 | 0 | |
| component_height-HeatmapList-method | 0 | 0 | 0 | |
| component_height-dispatch | 0 | 0 | 0 | |
| component_width-Heatmap-method | 0 | 0 | 0 | |
| component_width-HeatmapList-method | 0 | 0 | 0 | |
| component_width-dispatch | 0 | 0 | 0 | |
| copy_all-AnnotationFunction-method | 0 | 0 | 0 | |
| copy_all-SingleAnnotation-method | 0 | 0 | 0 | |
| copy_all-dispatch | 0 | 0 | 0 | |
| decorate_annotation | 0.28 | 0.00 | 0.29 | |
| decorate_column_dend | 0 | 0 | 0 | |
| decorate_column_names | 0 | 0 | 0 | |
| decorate_column_title | 0 | 0 | 0 | |
| decorate_dend | 0.15 | 0.00 | 0.16 | |
| decorate_dimnames | 0.36 | 0.00 | 0.36 | |
| decorate_heatmap_body | 0.08 | 0.00 | 0.08 | |
| decorate_row_dend | 0 | 0 | 0 | |
| decorate_row_names | 0 | 0 | 0 | |
| decorate_row_title | 0 | 0 | 0 | |
| decorate_title | 0.11 | 0.00 | 0.11 | |
| default_axis_param | 0 | 0 | 0 | |
| default_get_type | 0 | 0 | 0 | |
| dend_heights | 0 | 0 | 0 | |
| dend_xy | 0 | 0 | 0 | |
| dendrogramGrob | 0 | 0 | 0 | |
| densityHeatmap | 0.79 | 0.00 | 0.80 | |
| dim.Heatmap | 0 | 0 | 0 | |
| dist2 | 0.02 | 0.00 | 0.01 | |
| draw-AnnotationFunction-method | 0 | 0 | 0 | |
| draw-Heatmap-method | 0 | 0 | 0 | |
| draw-HeatmapAnnotation-method | 0 | 0 | 0 | |
| draw-HeatmapList-method | 0 | 0 | 0 | |
| draw-Legends-method | 0 | 0 | 0 | |
| draw-SingleAnnotation-method | 0 | 0 | 0 | |
| draw-dispatch | 0 | 0 | 0 | |
| draw_annotation-Heatmap-method | 0 | 0 | 0 | |
| draw_annotation_legend-HeatmapList-method | 0 | 0 | 0 | |
| draw_dend-Heatmap-method | 0.01 | 0.00 | 0.02 | |
| draw_dimnames-Heatmap-method | 0 | 0 | 0 | |
| draw_heatmap_body-Heatmap-method | 0 | 0 | 0 | |
| draw_heatmap_legend-HeatmapList-method | 0 | 0 | 0 | |
| draw_heatmap_list-HeatmapList-method | 0 | 0 | 0 | |
| draw_title-Heatmap-method | 0 | 0 | 0 | |
| draw_title-HeatmapList-method | 0 | 0 | 0 | |
| draw_title-dispatch | 0 | 0 | 0 | |
| extract_comb | 0 | 0 | 0 | |
| frequencyHeatmap | 0.35 | 0.00 | 0.34 | |
| full_comb_code | 0 | 0 | 0 | |
| getXY_in_parent_vp | 0 | 0 | 0 | |
| get_color_mapping_list-HeatmapAnnotation-method | 0 | 0 | 0 | |
| get_legend_param_list-HeatmapAnnotation-method | 0 | 0 | 0 | |
| grid.annotation_axis | 0 | 0 | 0 | |
| grid.boxplot | 0.01 | 0.00 | 0.02 | |
| grid.dendrogram | 0.52 | 0.02 | 0.53 | |
| grid.draw.Legends | 0.02 | 0.00 | 0.01 | |
| gt_render | 0.46 | 0.00 | 0.47 | |
| heatmap_legend_size-HeatmapList-method | 0 | 0 | 0 | |
| height.AnnotationFunction | 0.02 | 0.00 | 0.02 | |
| height.Heatmap | 0 | 0 | 0 | |
| height.HeatmapAnnotation | 0 | 0 | 0 | |
| height.HeatmapList | 0 | 0 | 0 | |
| height.Legends | 0 | 0 | 0 | |
| height.SingleAnnotation | 0 | 0 | 0 | |
| heightAssign.AnnotationFunction | 0 | 0 | 0 | |
| heightAssign.HeatmapAnnotation | 0 | 0 | 0 | |
| heightAssign.SingleAnnotation | 0 | 0 | 0 | |
| heightDetails.annotation_axis | 0 | 0 | 0 | |
| heightDetails.legend | 0 | 0 | 0 | |
| heightDetails.legend_body | 0 | 0 | 0 | |
| heightDetails.packed_legends | 0 | 0 | 0 | |
| ht_global_opt | 0 | 0 | 0 | |
| ht_opt | 0 | 0 | 0 | |
| ht_size | 0 | 0 | 0 | |
| is_abs_unit | 0 | 0 | 0 | |
| length.HeatmapAnnotation | 0 | 0 | 0 | |
| length.HeatmapList | 0 | 0 | 0 | |
| list_components | 0 | 0 | 0 | |
| list_to_matrix | 0 | 0 | 0 | |
| make_column_cluster-Heatmap-method | 0 | 0 | 0 | |
| make_comb_mat | 0 | 0 | 0 | |
| make_layout-Heatmap-method | 0 | 0 | 0 | |
| make_layout-HeatmapList-method | 0 | 0 | 0 | |
| make_layout-dispatch | 0 | 0 | 0 | |
| make_row_cluster-Heatmap-method | 0 | 0 | 0 | |
| map_to_colors-ColorMapping-method | 0 | 0 | 0 | |
| max_text_height | 0.02 | 0.00 | 0.02 | |
| max_text_width | 0 | 0 | 0 | |
| merge_dendrogram | 0.07 | 0.00 | 0.07 | |
| names.HeatmapAnnotation | 0.02 | 0.00 | 0.02 | |
| names.HeatmapList | 0 | 0 | 0 | |
| namesAssign.HeatmapAnnotation | 0 | 0 | 0 | |
| ncol.Heatmap | 0 | 0 | 0 | |
| nobs.AnnotationFunction | 0 | 0 | 0 | |
| nobs.HeatmapAnnotation | 0 | 0 | 0 | |
| nobs.SingleAnnotation | 0 | 0 | 0 | |
| normalize_comb_mat | 0 | 0 | 0 | |
| normalize_genomic_signals_to_bins | 0 | 0 | 0 | |
| nrow.Heatmap | 0 | 0 | 0 | |
| oncoPrint | 0 | 0 | 0 | |
| order.comb_mat | 0 | 0 | 0 | |
| packLegend | 0.04 | 0.00 | 0.04 | |
| pct_v_pct | 0 | 0 | 0 | |
| pheatmap | 0 | 0 | 0 | |
| pindex | 0 | 0 | 0 | |
| plot.Heatmap | 0 | 0 | 0 | |
| plot.HeatmapAnnotation | 0 | 0 | 0 | |
| plot.HeatmapList | 0 | 0 | 0 | |
| prepare-Heatmap-method | 0 | 0 | 0 | |
| print.comb_mat | 0 | 0 | 0 | |
| re_size-HeatmapAnnotation-method | 0 | 0 | 0 | |
| restore_matrix | 0.35 | 0.00 | 0.35 | |
| rowAnnotation | 0 | 0 | 0 | |
| row_anno_barplot | 0 | 0 | 0 | |
| row_anno_boxplot | 0 | 0 | 0 | |
| row_anno_density | 0 | 0 | 0 | |
| row_anno_histogram | 0 | 0 | 0 | |
| row_anno_points | 0 | 0 | 0 | |
| row_anno_text | 0 | 0 | 0 | |
| row_dend-Heatmap-method | 0.21 | 0.00 | 0.20 | |
| row_dend-HeatmapList-method | 0.53 | 0.00 | 0.54 | |
| row_dend-dispatch | 0 | 0 | 0 | |
| row_order-Heatmap-method | 0.25 | 0.01 | 0.26 | |
| row_order-HeatmapList-method | 0.57 | 0.00 | 0.58 | |
| row_order-dispatch | 0 | 0 | 0 | |
| set_component_height-Heatmap-method | 0 | 0 | 0 | |
| set_component_width-Heatmap-method | 0 | 0 | 0 | |
| set_name | 0 | 0 | 0 | |
| set_nameAssign | 0 | 0 | 0 | |
| set_size | 0.02 | 0.00 | 0.02 | |
| show-AnnotationFunction-method | 0 | 0 | 0 | |
| show-ColorMapping-method | 0 | 0 | 0 | |
| show-Heatmap-method | 0 | 0 | 0 | |
| show-HeatmapAnnotation-method | 0 | 0 | 0 | |
| show-HeatmapList-method | 0 | 0 | 0 | |
| show-SingleAnnotation-method | 0 | 0 | 0 | |
| show-dispatch | 0 | 0 | 0 | |
| size.AnnotationFunction | 0 | 0 | 0 | |
| size.HeatmapAnnotation | 0 | 0 | 0 | |
| size.SingleAnnotation | 0 | 0 | 0 | |
| sizeAssign.AnnotationFunction | 0 | 0 | 0 | |
| sizeAssign.HeatmapAnnotation | 0 | 0 | 0 | |
| sizeAssign.SingleAnnotation | 0 | 0 | 0 | |
| smartAlign2 | 0.17 | 0.00 | 0.17 | |
| str.comb_mat | 0 | 0 | 0 | |
| subset_gp | 0 | 0 | 0 | |
| subset_matrix_by_row | 0 | 0 | 0 | |
| subset_no | 0 | 0 | 0 | |
| subset_vector | 0 | 0 | 0 | |
| summary.Heatmap | 0 | 0 | 0 | |
| summary.HeatmapList | 0 | 0 | 0 | |
| t.comb_mat | 0 | 0 | 0 | |
| test_alter_fun | 0.03 | 0.00 | 0.03 | |
| unify_mat_list | 0 | 0 | 0 | |
| upset_left_annotation | 0 | 0 | 0 | |
| upset_right_annotation | 0 | 0 | 0 | |
| upset_top_annotation | 0 | 0 | 0 | |
| width.AnnotationFunction | 0 | 0 | 0 | |
| width.Heatmap | 0 | 0 | 0 | |
| width.HeatmapAnnotation | 0 | 0 | 0 | |
| width.HeatmapList | 0 | 0 | 0 | |
| width.Legends | 0.01 | 0.00 | 0.02 | |
| width.SingleAnnotation | 0 | 0 | 0 | |
| widthAssign.AnnotationFunction | 0 | 0 | 0 | |
| widthAssign.HeatmapAnnotation | 0 | 0 | 0 | |
| widthAssign.SingleAnnotation | 0 | 0 | 0 | |
| widthDetails.annotation_axis | 0 | 0 | 0 | |
| widthDetails.legend | 0 | 0 | 0 | |
| widthDetails.legend_body | 0 | 0 | 0 | |
| widthDetails.packed_legends | 0 | 0 | 0 | |