intensityBoxplot {qPLEXanalyzer}R Documentation

Intensity Distribution boxplot

Description

Intensity distribution boxplot of all the samples

Usage

intensityBoxplot(MSnSetObj, title="", sampleColours=NULL, colourBy="SampleGroup")

Arguments

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

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 boxplot 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)
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)

[Package qPLEXanalyzer version 1.0.4 Index]