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 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) 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)