volcanoPlot: Volcano plot.

In jtlovell/RNAseqDE: A pipeline for differential expression analyses in R

Description

volcanoPlot Make an expression volcano plot from log2-fold change and p-value data

Usage

volcanoPlot(pval, lfc, sig, alpha = 0.05, pointcols = c(rgb(1, 0, 0, 0.5),
  rgb(0, 0, 0, 0.5)), pchs = c(19, 19), cex = c(0.5, 0.5),
  legpos = "topright", leginset = c(-0.25, 0), ylab = "-log10 P-value",
  xlab = "log2 Fold Change", ...)

Arguments

pval	A vector of p-values
lfc	A vector of log-2 fold change (or similar data)
sig	Either a 0/1 binary vector of significance, or a vector of transformed p-values
alpha	If providing a vector of transformed p-values, this specifies the threshold for siginficance. Otherwise, not used.
pointcols	Vector of legnth 2. The first element indicates the color of significant points and the second the non sigificant points
pchs	Follows pointcols for point shapes
cex	Follows pointcols for point sizes
legpos	The position of the legend. Defaults to topright
leginset	How much the legend should be inset - defaults to just outside the plotting window.
ylab	The label for the y axis
xlab	The label for the x axis
...	additional arguments passed on to plot

Details

Using base R graphics, this function tabulates the number of significant values and plots

Value

a table with the number and direction of significance

Examples

## Not run: 
data(kidney) #from the simseq package
counts<-kidney$counts
counts<-counts[sample(1:nrow(counts),1000),]
info<-data.frame(rep=kidney$replic, treatment=kidney$treatment)
stats<-pipeLIMMA(counts=counts, info=info,
                 formula = " ~ treatment",
                 block=NULL,
                 getTopTable=T,
                 getEbayes=T)
stats<-stats$stats
volcanoPlot(pval=stats$ebayesPvalue_treatmentTumor,
            lfc=stats$treatmentTumor_logFC,
            sig=stats$ebayesQvalue_treatmentTumor,
            alpha=0.0005, pointcols=c("blue","grey"), pchs=c(4,6))

## End(Not run)

jtlovell/RNAseqDE documentation built on May 10, 2019, 8:06 a.m.