makeVolcanoPlot: Make a volcano plot

In kmuench/DESeqAid: DESeqAid: Kristin's favorite functions for her DESeq-based differential expression pipelines

Description

This function allows you to make a volcano plot from your DESeq results. It plots -log10 of your padjusted values against the log2 fold changes provided by DESeq. Note that this is not equipped to plot shrunken Log2FCs, just the default DESeq ones - but if you label the shrunken log2FCs as "log2FoldChange", the function will plot those instead. DE genes are colored red, and special other genes of interest colored in blue. It draws lines at pvalue = 0.05, log2FC = 1.32 (~2.5fold change) and 0.585 (~1.5fold change)

Usage

makeVolcanoPlot(volcanoPlotData, genesToHighlight, highlightGeneName,
  myTitle, myX, myY, currDate, nickname)

Arguments

volcanoPlotData	a data frame (preferably of the DESeq results output file). Contains columns named log2FoldChange, padj; and has row names that are genes
genesToHighlight	Genes that you'd like to color blue on this plot
highlightGeneName	What do you want to call these other points you're coloring blue?
myTitle	The title that will display over the plot
myX	X axis label
myY	Y axis label

Examples

makeVolcanoPlot(data.frame(results_sex_timepoint), amySexGenes[,2], 'Select Sex Genes', 'DE Genes based on interaction of Timepoint, Sex', 'Log2(Fold Change) relative to E12.5/M', '-log10(Adjusted p-value)')

kmuench/DESeqAid documentation built on Oct. 14, 2020, 4:45 a.m.