my.plotPCA {PCAPAM50} | R Documentation |
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)
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 |
Value
Returns an image containing:
pcafig |
The plot. |
See Also
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)
[Package PCAPAM50 version 1.0.1 Index]