intensityBoxplot {qPLEXanalyzer} | R Documentation |
Intensity distribution boxplot of all the samples
intensityBoxplot(MSnSetObj, title="", sampleColours=NULL, colourBy="SampleGroup")
MSnSetObj |
MSnSet; an object of class MSnSet |
title |
character; title of the plot |
sampleColours |
character: a named character vector of colors for samples |
colourBy |
character: column name from pData(MSnSetObj) to use for coloring samples |
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 boxplot 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) intensityBoxplot(MSnSet_data, title = "qPLEX_RIME_ER") # custom colours customCols <- rainbow(length(unique(pData(MSnSet_data)$SampleGroup))) names(customCols) <- unique(pData(MSnSet_data)$SampleGroup) intensityBoxplot(MSnSet_data, title = "qPLEX_RIME_ER", sampleColours = customCols)