plot_within_level_sample_MAs: Plot correlations of samples within a level of a group

In RNAseqQC: Quality Control for RNA-Seq Data

Plot correlations of samples within a level of a group

Description

For the given level, the gene-wise median over all samples is computed to obtain a reference sample. Then, each sample is plotted against the reference as MA-plot.

Usage

plot_within_level_sample_MAs(
  vsd,
  group,
  level,
  y_lim = 4,
  rasterise = FALSE,
  ...
)

Arguments

vsd	An object generated by DESeq2::vst()
group	A grouping variable, must be a column of colData(vsd)
level	A level of the grouping variable
y_lim	Y-axis limits, the axis will run from -y_lim to y_lim
rasterise	Whether to rasterise the points using ggrastr.
...	Other parameters passed on to ggrastr::rasterise

Value

A list of ggplot objects of the ggplot2 package that contains for each sample of the specified level the the sample vs reference MA-plot.

Examples

library("DESeq2")
set.seed(1)
dds <- makeExampleDESeqDataSet(n=1000, m=4, interceptMean=10)
colData(dds)$type <- c("A","A","B","B")
vsd <- vst(dds)
plot_within_level_sample_MAs(vsd, group="type", level="A")

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