PCAPAM50 (version 1.0.3)

my.plotPCA: Modeling after plotPCA of DESeq

Description

Modeling after plotPCA of DESeq

Usage

my.plotPCA(x, intgroup, ablne = 0,
           colours = c("red","hotpink","darkblue", "lightblue","red3","hotpink3",
           "royalblue3","lightskyblue3"),
           LINE.V = TRUE)

Value

Returns an image containing:

pcafig

The plot.

Arguments

x

An ExpressionSet object, with matrix data (x) in ‘assay(x)’, produced for example by ExpressionSet(assayData=Test.matrix, phenoData=phenoData)

intgroup

Subtype condition: a character vector of names in ‘colData(x)’ to use for grouping.

ablne

An x-axis coordinate for drawing a vertical line. Default is 0.

colours

Colors for subtypes present in the condition.

LINE.V

Determines whether or not to draw line. Default is TRUE.

See Also

prcomp, merge, set.seed

Examples

  library("Biobase")  
  
  data_path <- system.file("extdata", "Sample_IHC_PAM_Mat.Rdat", package = "PCAPAM50")
  load(data_path) # Loads Test.ihc and Test.matrix
  
  pData = data.frame(condition=Test.ihc$IHC)
  rownames(pData) = Test.ihc$PatientID
  phenoData = new("AnnotatedDataFrame", data=pData)#, varMetadata=Metadata
  XSet      = ExpressionSet(assayData=Test.matrix, phenoData=phenoData)
  my.plotPCA(XSet, intgroup=pData$condition, ablne=2.4,
  		colours = c("hotpink","darkblue","lightblue","lightblue3","red"),
  		LINE.V = TRUE)