An R library for creating Next-Generation Clustered Heat Maps (NG-CHM)
A docker image containing RStudio with this library preinstalled is available. Follow the instructions for using rstudio, but substitute "bmbroom/rstudio-ngchm" for the name of the repository.
To install this package into your own R system:
> install.packages("devtools") > devtools::install_github("bmbroom/tsvio") > devtools::install_github("bmbroom/NGCHMR", ref="stable")
You might also choose to install the beta version of the library, or for the really daring the master branch.
The installed library will be called NGCHM:
> library (NGCHM)
To use this library you need access to a Java application for generating standalone NG-CHMs and/or an NG-CHM server to which you can upload NG-CHMs.
To create standalone NG-CHMs you also need the Java application ShaidyMapGen.jar. The easiest way to get a copy is to download it from http://tcga.ngchm.net/NGCHM/ShaidyMapGen.jar. You can also build it from the source code. Once downloaded, set the environment variable SHAIDYMAPGEN to its location.
You will also need to create a configuration file describing, among other things, any NG-CHM server(s) to which you have access.
A basic guide to creating NG-CHMs using the library is available at http://bioinformatics.mdanderson.org/main/NG-CHM:NGCHMR-Using .
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