pcaPlot {qPLEXanalyzer} | R Documentation |
PCA plots of the samples within MSnset
pcaPlot( MSnSetObj, omitIgG = FALSE, sampleColours = NULL, transFunc = log2xplus1, transform = TRUE, colourBy = "SampleGroup", title = "", labelColumn = "BioRep", labelsize = 4, pointsize = 4, x.nudge = 4, x.PC = 1 )
MSnSetObj |
MSnSet; an object of class MSnSet |
omitIgG |
Logical: whether to remove IgG from the PCA plot |
sampleColours |
character: A named vector of colours for samples |
transFunc |
func: internal helper function for log transformation |
transform |
logical: whether to log transform intensities |
colourBy |
character: column name to use for colouring samples from
|
title |
character: title for the plot |
labelColumn |
character: column name from |
labelsize |
numeric: size of the labels |
pointsize |
numeric: size of plotting points |
x.nudge |
numeric: distance to move labels along the x-axis away from the plotting points |
x.PC |
numeric: The principle component to plot on the x-axis; the following PC will be plotted on the y-axis |
The column provided to the "colourBy" argument will be used to colour the samples. The colours will be determined using the function assignColours, alternatively the user may specify a named vector of colours using the "sampleColours" argument. The names of the "sampleColours" vector should match the unique values in the "colourBy" column.
An object created by ggplot
data(human_anno) data(exp3_OHT_ESR1) MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, metadata=exp3_OHT_ESR1$metadata_qPLEX1, indExpData=c(7:16), Sequences=2, Accessions=6) exprs(MSnSet_data) <- exprs(MSnSet_data)+0.01 pcaPlot(MSnSet_data, omitIgG = TRUE, labelColumn = "BioRep") # custom colours and PC2 v PC3 customCols <- rainbow(length(unique(pData(MSnSet_data)$SampleGroup))) names(customCols) <- unique(pData(MSnSet_data)$SampleGroup) pcaPlot(MSnSet_data, omitIgG = TRUE, labelColumn = "BioRep", sampleColours = customCols, x.PC=2)