plot_chromosome: Plot gene expression along a chromosome

In RNAseqQC: Quality Control for RNA-Seq Data

Plot gene expression along a chromosome

Description

Plot gene expression along a chromosome

Usage

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

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.

Value

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

Examples

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

RNAseqQC documentation built on July 1, 2024, 9:07 a.m.