intensityPlot: Intensity Distribution Plot

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

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 object created by ggplot

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)

crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.