plotCounts: Plot counts

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Plot counts

Description

Plot counts

Usage

plotCounts(object, ...)

## S4 method for signature 'DESeqAnalysis'
plotCounts(object, ..., samples = NULL, transform = FALSE)

## S4 method for signature 'DESeqDataSet'
plotCounts(object, ...)

## S4 method for signature 'DESeqTransform'
plotCounts(object, ...)

Arguments

object	Object.
...	Additional arguments.
samples	character. Sample identifiers.
transform	logical(1). Plot log2 variance-stabilized transform counts, defined internally in DESeqTransform object (see transform slot). If FALSE, plot the size factor adjusted counts from DESeqDataSet.

Value

• style = "facet": ggplot grouped by sampleName, with ggplot2::facet_wrap() applied to panel the samples.

• style = "wide": ggplot in wide format, with genes on the x-axis.

Functions

• plotCounts(DESeqAnalysis): Plot either DESeqDataSet normalized counts or DESeqTransform log2 variance-stabilized counts.

• plotCounts(DESeqDataSet): Plot size factor (i.e. library size) adjusted normalized counts. Arguments pass through to SummarizedExperiment method defined in AcidPlots package.

• plotCounts(DESeqTransform): Plot log2 variance-stabilized transformed counts.

Note

Updated 2021-03-15.

See Also

DESeq2::plotCounts.

Examples

data(deseq)

## Get genes from working example.
genes <- head(rownames(as(deseq, "DESeqDataSet")))
print(genes)

## DESeqAnalysis ====
plotCounts(deseq, genes = genes, style = "facet")
plotCounts(deseq, genes = genes, style = "wide")

steinbaugh/DESeqAnalysis documentation built on June 9, 2025, 7:56 a.m.