intensityPlot {qPLEXanalyzer} | R Documentation |
Intensity distribution plot of all the samples
intensityPlot(MSnSetObj, sampleColours=NULL, title="", colourBy="SampleGroup", transform=TRUE, xlab="log2(intensity)", trFunc=log2xplus1)
MSnSetObj |
MSnSet; an object of class MSnSet |
sampleColours |
character: a vector of colors for samples |
title |
character: title for the plot |
colourBy |
character: column name from pData(MSnSetObj) to use for coloring samples |
transform |
logical: whether to log transform intensities |
xlab |
character: label for x-axis |
trFunc |
func: internal helper function for log transformation |
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 intensity distribution plot for quantitative proteomics data.
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) intensityPlot(MSnSet_data, title = "qPLEX_RIME_ER") # custom colours customCols <- rainbow(length(unique(pData(MSnSet_data)$SampleGroup))) names(customCols) <- unique(pData(MSnSet_data)$SampleGroup) intensityPlot(MSnSet_data, title = "qPLEX_RIME_ER", sampleColours = customCols)