Principal component analysis plot

plotPCA(object, ...)

# S4 method for bcbioRNASeq
plotPCA(object, normalized = c("vst", "rlog"), ...)

Arguments

object

Object.

normalized

character(1) or logical(1). Normalization method to apply:

  • FALSE: Raw counts. When using a tximport-compatible caller, these are length scaled by default (see countsFromAbundance argument). When using a featureCounts-compatible caller, these are integer.

tximport caller-specific normalizations:

  • "tpm": Transcripts per million.

Additional gene-level-specific normalizations:

...

Passthrough to SummarizedExperiment method defined in AcidPlots. See AcidPlots::plotPCA() for details.

Value

ggplot.

Note

Updated 2020-09-15.

Author

Michael Steinbaugh

Examples

data(bcb) plotPCA(bcb, label = FALSE)
#> Using `vst` counts.
plotPCA(bcb, label = TRUE)
#> Using `vst` counts.