maVolPlot: MA or Volcano Plot

View source: R/maVolPlot.R

maVolPlotR Documentation

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.