pcaPlot: PCA plot

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

PCA plot

Description

PCA plots of the samples within MSnset

Usage

pcaPlot(
  MSnSetObj,
  omitIgG = FALSE,
  sampleColours = NULL,
  transFunc = log2xplus1,
  transform = TRUE,
  colourBy = "SampleGroup",
  title = "",
  labelColumn = "BioRep",
  labelsize = 4,
  pointsize = 4,
  x.nudge = 4,
  x.PC = 1
)

Arguments

MSnSetObj	MSnSet; an object of class MSnSet
omitIgG	Logical: whether to remove IgG from the PCA plot
sampleColours	character: A named vector of colours for samples
transFunc	func: internal helper function for log transformation
transform	logical: whether to log transform intensities
colourBy	character: column name to use for colouring samples from pData(MSnSetObj)
title	character: title for the plot
labelColumn	character: column name from pData(MSnSetObj) to use for labelling points on the plot or "none" to omit labels
labelsize	numeric: size of the labels
pointsize	numeric: size of plotting points
x.nudge	numeric: distance to move labels along the x-axis away from the plotting points
x.PC	numeric: The principle component to plot on the x-axis; the following PC will be plotted on the y-axis

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)
exprs(MSnSet_data) <- exprs(MSnSet_data)+0.01
pcaPlot(MSnSet_data, omitIgG = TRUE, labelColumn = "BioRep")

# custom colours and PC2 v PC3
customCols <- rainbow(length(unique(pData(MSnSet_data)$SampleGroup)))
names(customCols) <- unique(pData(MSnSet_data)$SampleGroup)
pcaPlot(MSnSet_data, 
        omitIgG = TRUE, 
        labelColumn = "BioRep", 
        sampleColours = customCols, 
        x.PC=2)

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