intensityBoxplot: Intensity Distribution boxplot

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

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 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)
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)

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