intensityPlot {qPLEXanalyzer}R Documentation

Intensity Distribution Plot

Description

Intensity distribution plot of all the samples

Usage

intensityPlot(MSnSetObj, sampleColours=NULL, title="", colourBy="SampleGroup", 
                          transform=TRUE, xlab="log2(intensity)",
                          trFunc=log2xplus1)

Arguments

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

Details

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.

Value

An intensity distribution plot for quantitative proteomics data.

Examples

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)

[Package qPLEXanalyzer version 1.4.0 Index]