plotExpressionPCA-methods: Create a PCA plot from a DGEList object

In steveped/spBioUtils: Various utility functions for bioinformatics

Description

Plot the PCA results from a DGEList

Usage

plotExpressionPCA(object, ...)

## S4 method for signature 'DGEList'
plotExpressionPCA(object, ..., .center = TRUE, .scale = FALSE)

## S4 method for signature 'SummarizedExperiment'
plotExpressionPCA(object, i = NULL, ..., .center = TRUE, .scale = FALSE)

Arguments

object	An object containing expression values (i.e. counts)
...	Used for passing parameters to autoplot.prcomp. These should be column names and can be passed to plotting aesthetics such as colour, shape and size.
.center	passed to prcomp
.scale	passed to prcomp
i	Identifies the assay to use in a SummarizedExperiment. Any assay other than counts will be used as provided, whilst the counts assay will be transformed into logCPM before performing the PCA.

Value

A ggplot2 object

Examples

library(edgeR)
y <- matrix(rnbinom(10000,mu=5,size=2), ncol=4)
d <- DGEList(counts=y, group=rep(1:2, each=2))
plotExpressionPCA(d, colour = "group")

library(SummarizedExperiment)
nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                     row.names=LETTERS[1:6])
se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
                            colData=colData)
plotExpressionPCA(se0, colour = "Treatment")

steveped/spBioUtils documentation built on Sept. 25, 2021, 7:22 p.m.