This package takes the original heatmap function and reduces the argument complexity. A heatmap is a false color image (image(t(x))) with a dendrogram added to the top and left side. Typically, reordering of the rows and columns according to some set of values (row or column means) within the restrictions imposed by the dendrogram is carried out.
This section covers installing the heatmap4 package from this UCSF-CBI repository. Installing this package will give you access to examples and help files for running the function “generate_heatmap” that you can use in R.
Please ensure that you have an access token to this heatmap4 repository before attempting to install the package (contact a owner/contributor to send you a personal access token).
install.packages("devtools")
library("devtools")
Note: R should show that it is loading the required package "usethis"
install_github("UCSF-CBI/heatmap4/heatmap4", auth_token = "xyz", build_vignettes = TRUE)
Note: make sure to include the “build_vignettes” argument, otherwise the package vignettes will not download. Also know that the auth_token given to you may be subject to change.
After downloading the package, you should have access to a heatmap4 help file as well as example the files that are in this repository.
After inputting your data set and assigning variables and values as needed, you can call the generate_heatmap function to build a heatmap based on a data set
library("heatmap4")
generate_heatmap(x, input_legend = FALSE)
In terminal: Use "cd" to change your directory to wherever the heatmap4 package is saved.
First enter "R" in order to use the R command build_vignettes.
R
build_vignettes("heatmap4")
After building vignettes you can check the package for errors and then build the package with the following commands.
check("heatmap4")
build("heatmap4")
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