Zuguang Gu
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ComplexHeatmap |
| Branch: RELEASE_3_12 |
| Last Commit: 0383bad |
| Last Changed Date: 2020-11-11 18:45:48 -0400 (Wed, 11 Nov 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:36 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the ComplexHeatmap package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 362/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ComplexHeatmap 2.6.2 (landing page) Zuguang Gu
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ComplexHeatmap |
| Version: 2.6.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ComplexHeatmap_2.6.2.tar.gz |
| StartedAt: 2021-05-06 00:34:11 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:41:33 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 441.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ComplexHeatmap.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ComplexHeatmap_2.6.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ComplexHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ComplexHeatmap’ version ‘2.6.2’
* 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 for sufficient/correct file permissions ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AnnotationFunction 6.3 0.094 6.403
* 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ComplexHeatmap ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘ComplexHeatmap’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ComplexHeatmap)
ComplexHeatmap.Rcheck/tests/test-annotation_axis.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 2.6.2
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.
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
3.050 0.205 3.238
ComplexHeatmap.Rcheck/tests/test-AnnotationFunction.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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))
>
>
> # 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")
>
>
> ##### 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))
>
>
> proc.time()
user system elapsed
22.455 0.538 23.080
ComplexHeatmap.Rcheck/tests/test-ColorMapping-class.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
3.371 0.215 3.565
ComplexHeatmap.Rcheck/tests/test-dendrogram.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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 1.14.0
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
Or contact: <tal.galili@gmail.com>
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
9.942 0.390 10.325
ComplexHeatmap.Rcheck/tests/test-gridtext.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 2.6.2
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.
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
4.972 0.262 5.218
ComplexHeatmap.Rcheck/tests/test-Heatmap-class.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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 1.14.0
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
Or contact: <tal.galili@gmail.com>
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
30.670 0.539 31.316
ComplexHeatmap.Rcheck/tests/test-Heatmap-cluster.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
3.237 0.208 3.430
ComplexHeatmap.Rcheck/tests/test-HeatmapAnnotation.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
17.022 0.375 17.417
ComplexHeatmap.Rcheck/tests/test-HeatmapList-class.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
22.434 0.391 22.833
ComplexHeatmap.Rcheck/tests/test-interactive.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
0.264 0.060 0.304
ComplexHeatmap.Rcheck/tests/test-Legend.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
4.922 0.261 5.165
ComplexHeatmap.Rcheck/tests/test-multiple-page.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
8.316 0.277 8.578
ComplexHeatmap.Rcheck/tests/test-oncoPrint.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 0.4.12 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 2.6.2 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. 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 11.017 0.320 11.345
ComplexHeatmap.Rcheck/tests/test-pheatmap.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 2.6.2
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.
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 supported in pheatmap -> Heatmap
translation, skip it.
>
> proc.time()
user system elapsed
30.689 0.375 31.158
ComplexHeatmap.Rcheck/tests/test-SingleAnnotation.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
5.014 0.249 5.246
ComplexHeatmap.Rcheck/tests/test-upset.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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
27.359 0.467 27.839
ComplexHeatmap.Rcheck/tests/test-utils.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.4.12
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 2.6.2
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.
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
3.024 0.193 3.246
ComplexHeatmap.Rcheck/tests/testthat-all.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
27.585 0.523 28.099
ComplexHeatmap.Rcheck/ComplexHeatmap-Ex.timings
| name | user | system | elapsed | |
| AdditiveUnit-class | 0.000 | 0.000 | 0.001 | |
| AdditiveUnit | 0 | 0 | 0 | |
| AnnotationFunction-class | 0.000 | 0.000 | 0.001 | |
| AnnotationFunction | 6.300 | 0.094 | 6.403 | |
| ColorMapping-class | 0 | 0 | 0 | |
| ColorMapping | 0.015 | 0.001 | 0.017 | |
| ComplexHeatmap-package | 0.001 | 0.000 | 0.000 | |
| Extract.AnnotationFunction | 0.032 | 0.002 | 0.034 | |
| Extract.Heatmap | 0.739 | 0.005 | 0.747 | |
| Extract.HeatmapAnnotation | 0.050 | 0.002 | 0.051 | |
| Extract.HeatmapList | 0.189 | 0.002 | 0.192 | |
| Extract.SingleAnnotation | 0.019 | 0.001 | 0.021 | |
| Extract.comb_mat | 0.013 | 0.001 | 0.014 | |
| Extract.gridtext | 0 | 0 | 0 | |
| Heatmap-class | 0 | 0 | 0 | |
| Heatmap | 0 | 0 | 0 | |
| HeatmapAnnotation-class | 0.000 | 0.000 | 0.001 | |
| HeatmapAnnotation | 0.000 | 0.000 | 0.001 | |
| HeatmapList-class | 0.000 | 0.000 | 0.001 | |
| HeatmapList | 0.000 | 0.000 | 0.001 | |
| Legend | 0.093 | 0.004 | 0.097 | |
| Legends-class | 0.010 | 0.000 | 0.011 | |
| Legends | 0 | 0 | 0 | |
| SingleAnnotation-class | 0.001 | 0.000 | 0.000 | |
| SingleAnnotation | 0.083 | 0.004 | 0.087 | |
| UpSet | 0.624 | 0.005 | 0.632 | |
| add.AdditiveUnit | 0.000 | 0.000 | 0.001 | |
| add_heatmap-Heatmap-method | 0.001 | 0.001 | 0.000 | |
| add_heatmap-HeatmapAnnotation-method | 0.001 | 0.000 | 0.000 | |
| add_heatmap-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| add_heatmap-dispatch | 0 | 0 | 0 | |
| adjust_dend_by_x | 0.023 | 0.004 | 0.027 | |
| adjust_heatmap_list-HeatmapList-method | 0 | 0 | 0 | |
| alter_graphic | 0.217 | 0.003 | 0.220 | |
| anno_barplot | 0.024 | 0.002 | 0.025 | |
| anno_block | 0.277 | 0.001 | 0.278 | |
| anno_boxplot | 0.030 | 0.001 | 0.031 | |
| anno_density | 0.559 | 0.015 | 0.576 | |
| anno_empty | 0.019 | 0.001 | 0.021 | |
| anno_histogram | 0.087 | 0.002 | 0.089 | |
| anno_horizon | 4.696 | 0.094 | 4.798 | |
| anno_image | 0.001 | 0.000 | 0.000 | |
| anno_joyplot | 0.456 | 0.021 | 0.480 | |
| anno_lines | 0.088 | 0.004 | 0.093 | |
| anno_link | 0.000 | 0.000 | 0.001 | |
| anno_mark | 0.596 | 0.005 | 0.601 | |
| anno_oncoprint_barplot | 0.001 | 0.000 | 0.000 | |
| anno_points | 0.027 | 0.002 | 0.028 | |
| anno_simple | 0.074 | 0.004 | 0.078 | |
| anno_summary | 0.433 | 0.003 | 0.437 | |
| anno_text | 0.076 | 0.004 | 0.113 | |
| anno_zoom | 0.570 | 0.004 | 0.574 | |
| annotation_axis_grob | 0.063 | 0.009 | 0.072 | |
| annotation_legend_size-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| attach_annotation-Heatmap-method | 0.937 | 0.005 | 0.945 | |
| c.ColorMapping | 0.003 | 0.000 | 0.003 | |
| c.HeatmapAnnotation | 0.036 | 0.001 | 0.038 | |
| cluster_within_group | 0.032 | 0.001 | 0.033 | |
| color_mapping_legend-ColorMapping-method | 0.000 | 0.001 | 0.000 | |
| columnAnnotation | 0.001 | 0.000 | 0.000 | |
| column_dend-Heatmap-method | 0.351 | 0.003 | 0.355 | |
| column_dend-HeatmapList-method | 1.380 | 0.013 | 1.396 | |
| column_dend-dispatch | 0 | 0 | 0 | |
| column_order-Heatmap-method | 0.428 | 0.003 | 0.432 | |
| column_order-HeatmapList-method | 1.460 | 0.008 | 1.471 | |
| column_order-dispatch | 0 | 0 | 0 | |
| comb_degree | 0.003 | 0.001 | 0.003 | |
| comb_name | 0.004 | 0.000 | 0.005 | |
| comb_size | 0.004 | 0.000 | 0.005 | |
| compare_pheatmap | 0.786 | 0.008 | 0.795 | |
| complement_size | 0 | 0 | 0 | |
| component_height-Heatmap-method | 0.000 | 0.001 | 0.001 | |
| component_height-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| component_height-dispatch | 0.000 | 0.000 | 0.001 | |
| component_width-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| component_width-HeatmapList-method | 0.001 | 0.000 | 0.000 | |
| component_width-dispatch | 0.001 | 0.000 | 0.000 | |
| copy_all-AnnotationFunction-method | 0.000 | 0.000 | 0.001 | |
| copy_all-SingleAnnotation-method | 0.000 | 0.001 | 0.000 | |
| copy_all-dispatch | 0 | 0 | 0 | |
| decorate_annotation | 0.343 | 0.002 | 0.345 | |
| decorate_column_dend | 0.000 | 0.001 | 0.001 | |
| decorate_column_names | 0.000 | 0.000 | 0.001 | |
| decorate_column_title | 0.000 | 0.001 | 0.000 | |
| decorate_dend | 0.169 | 0.001 | 0.170 | |
| decorate_dimnames | 0.253 | 0.002 | 0.256 | |
| decorate_heatmap_body | 0.180 | 0.002 | 0.181 | |
| decorate_row_dend | 0 | 0 | 0 | |
| decorate_row_names | 0.000 | 0.001 | 0.000 | |
| decorate_row_title | 0 | 0 | 0 | |
| decorate_title | 0.275 | 0.002 | 0.277 | |
| default_axis_param | 0.001 | 0.001 | 0.001 | |
| default_get_type | 0 | 0 | 0 | |
| dend_heights | 0 | 0 | 0 | |
| dend_xy | 0.021 | 0.001 | 0.022 | |
| dendrogramGrob | 0.000 | 0.000 | 0.001 | |
| densityHeatmap | 1.604 | 0.014 | 1.620 | |
| dim.Heatmap | 0 | 0 | 0 | |
| dist2 | 0.013 | 0.002 | 0.015 | |
| draw-AnnotationFunction-method | 0.000 | 0.001 | 0.001 | |
| draw-Heatmap-method | 0.001 | 0.000 | 0.001 | |
| draw-HeatmapAnnotation-method | 0.000 | 0.000 | 0.001 | |
| draw-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| draw-Legends-method | 0.019 | 0.001 | 0.019 | |
| draw-SingleAnnotation-method | 0 | 0 | 0 | |
| draw-dispatch | 0.000 | 0.001 | 0.001 | |
| draw_annotation-Heatmap-method | 0 | 0 | 0 | |
| draw_annotation_legend-HeatmapList-method | 0.001 | 0.000 | 0.000 | |
| draw_dend-Heatmap-method | 0 | 0 | 0 | |
| draw_dimnames-Heatmap-method | 0 | 0 | 0 | |
| draw_heatmap_body-Heatmap-method | 0.001 | 0.000 | 0.000 | |
| draw_heatmap_legend-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| draw_heatmap_list-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| draw_title-Heatmap-method | 0.000 | 0.001 | 0.001 | |
| draw_title-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| draw_title-dispatch | 0.001 | 0.000 | 0.001 | |
| extract_comb | 0.004 | 0.000 | 0.004 | |
| full_comb_code | 0.003 | 0.001 | 0.003 | |
| getXY_in_parent_vp | 0.020 | 0.001 | 0.021 | |
| get_color_mapping_list-HeatmapAnnotation-method | 0 | 0 | 0 | |
| get_legend_param_list-HeatmapAnnotation-method | 0.001 | 0.000 | 0.000 | |
| grid.annotation_axis | 0 | 0 | 0 | |
| grid.boxplot | 0.007 | 0.001 | 0.008 | |
| grid.dendrogram | 0.850 | 0.033 | 0.885 | |
| grid.draw.Legends | 0.019 | 0.000 | 0.020 | |
| gt_render | 0.980 | 0.012 | 0.996 | |
| heatmap_legend_size-HeatmapList-method | 0.001 | 0.000 | 0.001 | |
| height.AnnotationFunction | 0.007 | 0.000 | 0.007 | |
| height.Heatmap | 0.000 | 0.000 | 0.001 | |
| height.HeatmapAnnotation | 0 | 0 | 0 | |
| height.HeatmapList | 0 | 0 | 0 | |
| height.Legends | 0.027 | 0.000 | 0.026 | |
| height.SingleAnnotation | 0 | 0 | 0 | |
| heightAssign.AnnotationFunction | 0.000 | 0.000 | 0.001 | |
| heightAssign.HeatmapAnnotation | 0 | 0 | 0 | |
| heightAssign.SingleAnnotation | 0 | 0 | 0 | |
| heightDetails.annotation_axis | 0.000 | 0.000 | 0.001 | |
| heightDetails.legend | 0 | 0 | 0 | |
| heightDetails.legend_body | 0.000 | 0.000 | 0.001 | |
| heightDetails.packed_legends | 0 | 0 | 0 | |
| ht_global_opt | 0.001 | 0.000 | 0.000 | |
| ht_opt | 0.008 | 0.001 | 0.010 | |
| ht_pos_on_device | 0.001 | 0.000 | 0.002 | |
| ht_shiny | 0.002 | 0.000 | 0.003 | |
| ht_size | 0.001 | 0.000 | 0.000 | |
| is_abs_unit | 0.002 | 0.000 | 0.002 | |
| length.HeatmapAnnotation | 0 | 0 | 0 | |
| length.HeatmapList | 0.000 | 0.000 | 0.001 | |
| list_components | 0.000 | 0.000 | 0.001 | |
| list_to_matrix | 0.002 | 0.002 | 0.003 | |
| make_column_cluster-Heatmap-method | 0 | 0 | 0 | |
| make_comb_mat | 0.006 | 0.002 | 0.007 | |
| make_layout-Heatmap-method | 0.001 | 0.000 | 0.000 | |
| 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 | 0.023 | 0.001 | 0.024 | |
| max_text_height | 0.003 | 0.000 | 0.003 | |
| max_text_width | 0.002 | 0.000 | 0.002 | |
| merge_dendrogram | 0.131 | 0.003 | 0.136 | |
| names.HeatmapAnnotation | 0.023 | 0.000 | 0.022 | |
| names.HeatmapList | 0 | 0 | 0 | |
| namesAssign.HeatmapAnnotation | 0.021 | 0.001 | 0.022 | |
| ncol.Heatmap | 0 | 0 | 0 | |
| nobs.AnnotationFunction | 0.006 | 0.000 | 0.006 | |
| nobs.HeatmapAnnotation | 0.000 | 0.001 | 0.001 | |
| nobs.SingleAnnotation | 0 | 0 | 0 | |
| normalize_comb_mat | 0.000 | 0.001 | 0.000 | |
| nrow.Heatmap | 0 | 0 | 0 | |
| oncoPrint | 0.001 | 0.000 | 0.001 | |
| order.comb_mat | 0.000 | 0.000 | 0.001 | |
| packLegend | 0.096 | 0.003 | 0.099 | |
| pct_v_pct | 0.000 | 0.001 | 0.001 | |
| pheatmap | 0.000 | 0.000 | 0.001 | |
| pindex | 0.006 | 0.001 | 0.007 | |
| prepare-Heatmap-method | 0 | 0 | 0 | |
| print.comb_mat | 0.000 | 0.000 | 0.001 | |
| re_size-HeatmapAnnotation-method | 0.000 | 0.000 | 0.001 | |
| restore_matrix | 0.538 | 0.004 | 0.543 | |
| rowAnnotation | 0.000 | 0.000 | 0.001 | |
| row_anno_barplot | 0.000 | 0.000 | 0.001 | |
| row_anno_boxplot | 0.001 | 0.000 | 0.001 | |
| row_anno_density | 0.000 | 0.001 | 0.001 | |
| row_anno_histogram | 0 | 0 | 0 | |
| row_anno_points | 0 | 0 | 0 | |
| row_anno_text | 0 | 0 | 0 | |
| row_dend-Heatmap-method | 0.398 | 0.003 | 0.402 | |
| row_dend-HeatmapList-method | 1.071 | 0.007 | 1.079 | |
| row_dend-dispatch | 0.001 | 0.000 | 0.001 | |
| row_order-Heatmap-method | 0.446 | 0.003 | 0.450 | |
| row_order-HeatmapList-method | 1.356 | 0.007 | 1.363 | |
| row_order-dispatch | 0 | 0 | 0 | |
| selectArea | 0.001 | 0.000 | 0.001 | |
| selectPosition | 0.001 | 0.000 | 0.000 | |
| set_component_height-Heatmap-method | 0.001 | 0.000 | 0.001 | |
| set_component_width-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| set_name | 0.002 | 0.000 | 0.002 | |
| set_nameAssign | 0.006 | 0.001 | 0.007 | |
| set_size | 0.003 | 0.001 | 0.003 | |
| show-AnnotationFunction-method | 0.000 | 0.001 | 0.000 | |
| show-ColorMapping-method | 0.001 | 0.000 | 0.000 | |
| show-Heatmap-method | 0.001 | 0.000 | 0.001 | |
| show-HeatmapAnnotation-method | 0.001 | 0.001 | 0.000 | |
| show-HeatmapList-method | 0 | 0 | 0 | |
| show-SingleAnnotation-method | 0 | 0 | 0 | |
| show-dispatch | 0.000 | 0.001 | 0.001 | |
| size.AnnotationFunction | 0.009 | 0.000 | 0.010 | |
| size.HeatmapAnnotation | 0 | 0 | 0 | |
| size.SingleAnnotation | 0 | 0 | 0 | |
| sizeAssign.AnnotationFunction | 0.004 | 0.000 | 0.004 | |
| sizeAssign.HeatmapAnnotation | 0.000 | 0.001 | 0.001 | |
| sizeAssign.SingleAnnotation | 0.001 | 0.000 | 0.000 | |
| smartAlign2 | 0.394 | 0.004 | 0.401 | |
| str.comb_mat | 0.001 | 0.000 | 0.000 | |
| subset_gp | 0.001 | 0.000 | 0.000 | |
| subset_matrix_by_row | 0.000 | 0.000 | 0.001 | |
| subset_vector | 0.000 | 0.000 | 0.001 | |
| summary.Heatmap | 0 | 0 | 0 | |
| summary.HeatmapList | 0 | 0 | 0 | |
| t.comb_mat | 0.007 | 0.001 | 0.008 | |
| test_alter_fun | 0.081 | 0.002 | 0.082 | |
| unify_mat_list | 0.000 | 0.001 | 0.000 | |
| upset_right_annotation | 0 | 0 | 0 | |
| upset_top_annotation | 0.000 | 0.000 | 0.001 | |
| width.AnnotationFunction | 0.007 | 0.001 | 0.007 | |
| width.Heatmap | 0 | 0 | 0 | |
| width.HeatmapAnnotation | 0.000 | 0.000 | 0.001 | |
| width.HeatmapList | 0 | 0 | 0 | |
| width.Legends | 0.022 | 0.000 | 0.022 | |
| width.SingleAnnotation | 0.000 | 0.001 | 0.000 | |
| widthAssign.AnnotationFunction | 0 | 0 | 0 | |
| widthAssign.HeatmapAnnotation | 0.000 | 0.001 | 0.000 | |
| widthAssign.SingleAnnotation | 0.000 | 0.000 | 0.001 | |
| widthDetails.annotation_axis | 0.001 | 0.000 | 0.000 | |
| widthDetails.legend | 0 | 0 | 0 | |
| widthDetails.legend_body | 0 | 0 | 0 | |
| widthDetails.packed_legends | 0.001 | 0.000 | 0.000 | |