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 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) 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)