In CharlesJB/heatmapHIV: Produce heatmaps for RNA-Seq HIV data

heatmapHIV: A package to facilitate the production of heatmaps

Introduction

This short vignette will show how to use the heatmapHIV package.

suppressMessages(library(heatmapHIV))

The main function is named heatmapHIV and will produce an heatmap using the following files as input:

• A RPKM or raw data matrix in tsv format.
• A list of gene in csv format (one gene by line).

We need to give the function the path to both filename.

For this demo, we will use toy examples available with this package:

rpkm <- get_toy_rpkm()
gene_list <- get_toy_gene_list()
rpkm
gene_list

Once we have the path to the file, producing an heatmap is very simple:

heatmapHIV(rpkm, gene_list)

By default, the sequences will be clustered on columns only. It is also possible to use the filter parameter to sort the rows based on the mean RPKM of a subset of columns. The filter param is a character string that that is found in the names of the columns we wish to use to sort the rows.

For instance, if we wish to order the matrix using the columns that contains the pattern Exp:

heatmapHIV(rpkm, gene_list, filter = "Exp")

Finally, the final matrix used to produce the heatmap is silently returned:

current_matrix <- heatmapHIV(rpkm, gene_list)
class(current_matrix)
dim(current_matrix)

CharlesJB/heatmapHIV documentation built on May 6, 2019, 9:58 a.m.