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Plot counts

Source: R/AllGenerics.R, R/plotCounts-methods.R
plotCounts.Rd

Plot counts

Usage

plotCounts(object, ...)

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

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

# S4 method for 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)
#> [1] "gene1" "gene2" "gene3" "gene4" "gene5" "gene6"

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

plotCounts(deseq, genes = genes, style = "wide")