DESeq2 (version 1.12.3)

plotPCA: Sample PCA plot for transformed data

Description

This plot helps to check for batch effects and the like.

Usage

"plotPCA"(object, intgroup = "condition", ntop = 500, returnData = FALSE)

Arguments

object

a DESeqTransform object, with data in assay(x), produced for example by either rlog or varianceStabilizingTransformation.

intgroup

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

ntop

number of top genes to use for principal components, selected by highest row variance

returnData

should the function only return the data.frame of PC1 and PC2 with intgroup covariates for custom plotting (default is FALSE)

Value

An object created by ggplot, which can be assigned and further customized.

Examples

# using rlog transformed data:
dds <- makeExampleDESeqDataSet(betaSD=1)
rld <- rlog(dds)
plotPCA(rld)

# also possible to perform custom transformation:
dds <- estimateSizeFactors(dds)
# shifted log of normalized counts
se <- SummarizedExperiment(log2(counts(dds, normalized=TRUE) + 1),
                           colData=colData(dds))
# the call to DESeqTransform() is needed to
# trigger our plotPCA method.
plotPCA( DESeqTransform( se ) )