RNAseqQC (version 0.2.1)

plot_chromosome: Plot gene expression along a chromosome

Description

Plot gene expression along a chromosome

Usage

plot_chromosome(vsd, chr, scale = FALSE, trunc_val = NULL)

Value

A Heatmap-class object of the ComplexHeatmap package that contains the heatmap of expression values.

Arguments

vsd

An object generated by DESeq2::vst()

chr

A string denoting a chromosome as annotated by ENSEMBL, e.g. '1', '2', 'X', 'Y', 'MT'

scale

Whether to scale the columns of the heatmap

trunc_val

Truncate the expression matrix to this value prior to plotting. This is useful if some very high expression values dominate the heatmap. By default, the heatmap is truncated to expression values at most 3 standard deviations from the mean.

Examples

library("DESeq2")
chr1 <- T47D[which(mcols(T47D)$chromosome=="1"),]
vsd <- vst(chr1)
plot_chromosome(vsd, chr="1")