|
mitch.Rcheck/tests_i386/test-mitch.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("mitch")
> library("testthat")
>
> test_that("multiplication works", {
+ expect_equal(2 * 2, 4)
+ })
Test passed
>
> # 1d
> data(rna,genesetsExample)
> y<-mitch_import(rna,DEtype="edgeR")
The input is a single dataframe; one contrast only. Converting
it to a list for you.
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small
p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="1d.pdf")
null device
1
> if (file.exists("1d.html")) { unlink("1d.html") }
> mitch_report(res,"1d.html")
Dataset saved as " C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv/1d.rds ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
Contour plot does not apply to unidimensional analysis.
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_i386/mitch.utf8.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc2dfc6a206a48.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv\rmarkdown-str2dfc2b7b5481.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
Output created: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv/mitch_report.html
[1] TRUE
>
> test_that("1d works", {
+ expect_equal( length(which(res$enrichment_result$p.adjustANOVA<0.1)) ,1)
+ expect_true(file.info("1d.pdf")$size>10000)
+ expect_true(file.info("1d.html")$size>1000000)
+ })
Test passed
>
> unlink("1d.html")
> unlink("1d.pdf")
>
>
> # 1d part 2 to make sure that saving files at a different location works
> MYPATH=paste(getwd(),"/1d.html",sep="")
> if (file.exists("1d.html")) { unlink("1d.html") }
> mitch_report(res,MYPATH)
Dataset saved as " C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv/1d.rds ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
Contour plot does not apply to unidimensional analysis.
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_i386/mitch.utf8.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc2dfc3581770c.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv\rmarkdown-str2dfc4f0041a5.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
Output created: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv/mitch_report.html
[1] TRUE
>
> test_that("1d works", {
+ expect_true(file.info("1d.html")$size>1000000)
+ })
Test passed
>
> unlink("1d.html")
>
>
>
> # 2d
> data(rna,k9a,genesetsExample)
> x<-list("rna"=rna,"k9a"=k9a)
> y<-mitch_import(x,DEtype="edgeR")
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small
p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="2d.pdf")
null device
1
> if (file.exists("2d.html")) { unlink("2d.html") }
> mitch_report(res,"2d.html")
Dataset saved as " C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv/2d.rds ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_i386/mitch.utf8.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc2dfc7e23189f.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv\rmarkdown-str2dfc20815409.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
Output created: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv/mitch_report.html
[1] TRUE
>
> test_that("2d works", {
+ expect_equal( length(which(res$enrichment_result$p.adjustMANOVA<0.1)) ,1)
+ expect_true(file.info("2d.pdf")$size>100000)
+ expect_true(file.info("2d.html")$size>1000000)
+ })
Test passed
>
> unlink("2d.html")
> unlink("2d.pdf")
>
> # 3d
> data(rna,k9a,k36a,genesetsExample)
> x<-list("rna"=rna,"k9a"=k9a,"k36a"=k36a)
> y<-mitch_import(x,DEtype="edgeR")
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small
p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="3d.pdf")
null device
1
> if (file.exists("3d.html")) { unlink("3d.html") }
> mitch_report(res,"3d.html")
Dataset saved as " C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv/3d.rds ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
No significant enrichments found.
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_i386/mitch.utf8.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc2dfc1be462fb.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv\rmarkdown-str2dfc2b394264.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
Output created: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpwZLPkv/mitch_report.html
[1] TRUE
>
> test_that("3d works", {
+ expect_equal( length(which(res$enrichment_result$p.adjustMANOVA<0.1)) ,1)
+ expect_true(file.info("3d.pdf")$size>100000)
+ expect_true(file.info("3d.html")$size>1000000)
+ })
Test passed
>
> unlink("3d.html")
> unlink("3d.pdf")
>
>
>
> proc.time()
user system elapsed
59.53 5.23 74.93
|
mitch.Rcheck/tests_x64/test-mitch.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("mitch")
> library("testthat")
>
> test_that("multiplication works", {
+ expect_equal(2 * 2, 4)
+ })
Test passed
>
> # 1d
> data(rna,genesetsExample)
> y<-mitch_import(rna,DEtype="edgeR")
The input is a single dataframe; one contrast only. Converting
it to a list for you.
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small
p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="1d.pdf")
null device
1
> if (file.exists("1d.html")) { unlink("1d.html") }
> mitch_report(res,"1d.html")
Dataset saved as " C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8/1d.rds ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
Contour plot does not apply to unidimensional analysis.
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_x64/mitch.utf8.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc22446428339.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8\rmarkdown-str2244772813b3.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
Output created: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8/mitch_report.html
[1] TRUE
>
> test_that("1d works", {
+ expect_equal( length(which(res$enrichment_result$p.adjustANOVA<0.1)) ,1)
+ expect_true(file.info("1d.pdf")$size>10000)
+ expect_true(file.info("1d.html")$size>1000000)
+ })
Test passed
>
> unlink("1d.html")
> unlink("1d.pdf")
>
>
> # 1d part 2 to make sure that saving files at a different location works
> MYPATH=paste(getwd(),"/1d.html",sep="")
> if (file.exists("1d.html")) { unlink("1d.html") }
> mitch_report(res,MYPATH)
Dataset saved as " C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8/1d.rds ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
Contour plot does not apply to unidimensional analysis.
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_x64/mitch.utf8.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc2244e224a47.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8\rmarkdown-str22444f4e6e2a.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
Output created: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8/mitch_report.html
[1] TRUE
>
> test_that("1d works", {
+ expect_true(file.info("1d.html")$size>1000000)
+ })
Test passed
>
> unlink("1d.html")
>
>
>
> # 2d
> data(rna,k9a,genesetsExample)
> x<-list("rna"=rna,"k9a"=k9a)
> y<-mitch_import(x,DEtype="edgeR")
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small
p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="2d.pdf")
null device
1
> if (file.exists("2d.html")) { unlink("2d.html") }
> mitch_report(res,"2d.html")
Dataset saved as " C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8/2d.rds ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_x64/mitch.utf8.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc224427c342b7.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8\rmarkdown-str224427756ceb.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
Output created: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8/mitch_report.html
[1] TRUE
>
> test_that("2d works", {
+ expect_equal( length(which(res$enrichment_result$p.adjustMANOVA<0.1)) ,1)
+ expect_true(file.info("2d.pdf")$size>100000)
+ expect_true(file.info("2d.html")$size>1000000)
+ })
Test passed
>
> unlink("2d.html")
> unlink("2d.pdf")
>
> # 3d
> data(rna,k9a,k36a,genesetsExample)
> x<-list("rna"=rna,"k9a"=k9a,"k36a"=k36a)
> y<-mitch_import(x,DEtype="edgeR")
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small
p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="3d.pdf")
null device
1
> if (file.exists("3d.html")) { unlink("3d.html") }
> mitch_report(res,"3d.html")
Dataset saved as " C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8/3d.rds ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
No significant enrichments found.
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.12-bioc/meat/mitch.Rcheck/tests_x64/mitch.utf8.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc2244384d3323.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8\rmarkdown-str224427d4a9d.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
Output created: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpkBYdi8/mitch_report.html
[1] TRUE
>
> test_that("3d works", {
+ expect_equal( length(which(res$enrichment_result$p.adjustMANOVA<0.1)) ,1)
+ expect_true(file.info("3d.pdf")$size>100000)
+ expect_true(file.info("3d.html")$size>1000000)
+ })
Test passed
>
> unlink("3d.html")
> unlink("3d.pdf")
>
>
>
> proc.time()
user system elapsed
68.96 5.20 82.82
|
