DESeq2 (version 1.12.3)

plotCounts: Plot of normalized counts for a single gene on log scale

Description

Note: normalized counts plus a pseudocount of 0.5 are shown.

Usage

plotCounts(dds, gene, intgroup = "condition", normalized = TRUE, transform = FALSE, main, xlab = "group", returnData = FALSE, replaced = FALSE, ...)

Arguments

dds

a DESeqDataSet

gene

a character, specifying the name of the gene to plot

intgroup

interesting groups: a character vector of names in colData(x) to use for grouping

normalized

whether the counts should be normalized by size factor (default is TRUE)

transform

whether to present log2 counts (TRUE) or to present the counts on the log scale (FALSE, default)

main

as in 'plot'

xlab

as in 'plot'

returnData

should the function only return the data.frame of counts and covariates for custom plotting (default is FALSE)

replaced

use the outlier-replaced counts if they exist

...

arguments passed to plot

Examples

dds <- makeExampleDESeqDataSet()
plotCounts(dds, "gene1")