makeVolcPlot: Function to Create a Volcano Plot

In bhklab/CMapBox:

Description

This function will create a volcano plot that has the top and bottom 5 genes (according to gene estimates) labelled. Alternatively, users can turn off the plotting option in which case just the info used to make the plot will be returned.

Usage

makeVolcPlot(genesEst, genesSymb, genesP, genesId = NULL,
  idsOfInt = NULL, makePlot = TRUE, topGenes = 5)

Arguments

genesEst	a numeric vector with the estimates (typically LogFC) for the genes
genesSymb	a character vector with the gene symbols for the gene estimates provided
genesP	a numeric vector with the p values for the gene estimates provided
genesId	a character vector with gene Ids for the gene estimates provided. The gene Ids must be of the same type as IdsOfInt. If not provided genes outside of IdsOfInt cannot be removed
idsOfInt	a list of Ids to be kept when making the volcano plots, if not provided all Ids will be used
makePlot	a boolean that, if TRUE, will create a volcano plot. Default is TRUE
topGenes	The number of the most positive and negative genes, accordin to geneEst, to label on the volcano plot and/or return. Default is 5

Value

a list containing the frame used for the volcano plot, a frame with info for the top positive genes labelled in the volcano plot, and a frame with info for the top negative genes labelled in the volcano plot

Examples

#add example with CMAP here
data("geneDataGwc")
geneDataClean = mapGenes(geneIds = geneDataGwc$symbol, geneEsts = geneDataGwc$logFC, pvals = geneDataGwc$P.Value, forRankAndPlot = TRUE)
volcPlotData = makeVolcPlot(genesEst = geneDataClean$geneEsts, genesSymb = geneDataClean$symbol, genesP = geneDataClean$pvals)

bhklab/CMapBox documentation built on Nov. 6, 2019, 8:07 p.m.