README.md

In TomKellyGenetics/heatmap.2x: Enhanced Heatmap (with annotation bar matrices)

Enhanced Heatmap

This is the master branch. This branch is recommended for most colour matrix annotation, additional functionality is possible in the test version if needed.

Altered version of heatmap.2 by Mik Black and Tom Kelly at the University of Otago

Modifications to the R function heatmap.2 {gplots}

Requires R packages gplots and gtools

• heatmap.2x: enables multiple colorbars for ColSideColors with rbind, rownames are labels

• heatmap.2x: enables multiple colorbars for RowSideColors with cbind, colnames are labels

• master branch recommended for most column matrix annotation. Functionality comparable to heatmap.3 https://gist.github.com/nachocab/3853004 - note: annotation matrix dimensions differ from heatmap.3

• test branch restores additional functionality for customisation of axes labels, key labels, reorder functions, extra functions, and symmetric breaks -- these have been merged into the supr branch. The test branch is recommended for near complete functionality of heatmap.2 with additional matrix annotation. However many of these changes have not been thoroughly tested and the test branch should only be used if issues arise from lack of functionality of the master branch.

To get the modified version from github:

# install.packages("devtools")
devtools::install_github("TomKellyGenetics/heatmap.2x", ref="master")

To get the modified version from github (with various functions of heatmap.2 restored):

# install.packages("devtools")
devtools::install_github("TomKellyGenetics/heatmap.2x", ref="test")

To get the current released version from CRAN:

install.packages("gplots")

Citation of original package: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2015). gplots: Various R Programming Tools for Plotting Data. R package version 2.17.0. http://CRAN.R-project.org/package=gplots

Running

See the relevant vignettes for more details:

https://rawgit.com/TomKellyGenetics/heatmap.2x/master/vignettes/heatmap_annotation.html https://rawgit.com/TomKellyGenetics/heatmap.2x/master/vignettes/heatmap_golub.html

heatmap.2x works in much the same manner as heatmap.2

• heatmap.2x::heatmap.2x() generates a heatmap, takes the same arguments as gplots::heatmap.2() to plot a heatmap with colour bar annotation (optional) using ColSideCols and RowSideCols vectors.

• heatmap.2x::heatmap.2x() also enables multiple colour bar annotation (optional) using ColSideCols and RowSideCols a matrices with ncols(x) columns or nrows(x) rows respectively. ColSideCols is an ncols(x)*n matrix for n color bars. RowSideCols is an m*nrows(x) matrix for m color bars.

• heatmap.2x::heatmap.2x() also takes additional arguments to specify cexLab and colbarsize to modify the size colours separately the width and labels of the colour bars respectively.

Stable branch

Note there is a stable branch to try the added annotation bars with very few changes to heatmap.2 code from gplots:

# install.packages("devtools")
devtools::install_github("TomKellyGenetics/heatmap.2x", ref="stable")

For development history prior to package documentation, see the original repo: https://github.com/TomKellyGenetics/R-Heatmap-Functions/commits?author=TomKellyGenetics

TomKellyGenetics/heatmap.2x documentation built on July 8, 2019, 4:38 a.m.