rliPlot: Relative log intensity plot

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

Relative log intensity plot

Description

Relative log intensity (RLI) plots of the samples within MSnset

Usage

rliPlot(
  MSnSetObj,
  title = "",
  sampleColours = NULL,
  colourBy = "SampleGroup",
  omitIgG = TRUE
)

Arguments

MSnSetObj	MSnSet; an object of class MSnSet
title	character: title for the plot
sampleColours	character: a named vector of colours for samples
colourBy	character: column name to use for colouring samples from pData(MSnSetObj)
omitIgG	logical: whether to remove IgG from the RLI plot

Details

An RLI-plot is a boxplot that can be used to visualise unwanted variation in a data set. It is similar to the relative log expression plot developed for microarray analysis - see Gandolfo and Speed (2018). Rather than examining gene expression, the RLI plot uses the MS intensities for each peptide or the summarised protein intensities.

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 object created by ggplot

References

Gandolfo LC, Speed TP (2018) RLE plots: Visualizing unwanted variation in high dimensional data. PLoS ONE 13(2): e0191629. https://doi.org/10.1371/journal.pone.0191629

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)
rliPlot(MSnSet_data, title = "qPLEX_RIME_ER")

# custom colours
customCols <- rainbow(length(unique(pData(MSnSet_data)$SampleGroup)))
names(customCols) <- unique(pData(MSnSet_data)$SampleGroup)
rliPlot(MSnSet_data, title = "qPLEX_RIME_ER", sampleColours = customCols)

crukci-bioinformatics/qPLEXanalyzer documentation built on Oct. 23, 2023, 2:27 a.m.