maVolPlot: MA or Volcano Plot

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

MA or Volcano Plot

Description

MA or Volcano plot of differential statistics results

Usage

maVolPlot(
  diffstats,
  contrast,
  title = "",
  controlGroup = NULL,
  selectedGenes = NULL,
  fdrCutOff = 0.05,
  lfcCutOff = 1,
  controlLfcCutOff = 1,
  plotType = "MA"
)

Arguments

diffstats	list; output of computeDiffStats function
contrast	character; contrast of interest to plot differential statistics results
title	character: title for the plot
controlGroup	character; control group such as IgG
selectedGenes	character: a vector defining genes to plot
fdrCutOff	numeric: False Discovery Rate (adj.P.Val) cut off
lfcCutOff	numeric: Log Fold Change (log2FC) cutoff for
controlLfcCutOff	numeric: only plot genes above controlLogFoldChange cutoff
plotType	character: which type of plot to generate: "MA" or "Volcano"

Details

Genes determined as significant according to the Log Fold Change and False Discovery Rate cutoffs are highlighted in red.

A user specified selection of genes can be highlighted by passing a character vector of Accessions to the selectedGenes argument. The contents of this vector will be matched with the Accessions column of the diffstats object to identify rows to highlight. These will be plotted in blue and labeled with the contents of the GeneSymbol column. Note that if the GeneSymbol for a selected gene is missing, no label will be apparent.

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)
MSnset_norm <- groupScaling(MSnSet_data, scalingFunction=median)
MSnset_Pnorm <- summarizeIntensities(MSnset_norm, sum, human_anno)
contrasts <- c(tam.24h_vs_vehicle = "tam.24h - vehicle")
diffstats <- computeDiffStats(MSnset_Pnorm, contrasts=contrasts)
maVolPlot(diffstats, contrast = contrasts, plotType="MA")
maVolPlot(diffstats, contrast = contrasts, plotType="Volcano")

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