Create a volcano plot on EBSeq output

The differential expression analysis program EBSeq produces a number of data objects as part of the workflow, but there aren’t many options for visualization of the data.

The authors suggest the use of heatmap.2 in R:

heatmap.2(NormalizedMatrix[GenesOfInterest,], scale=”row”, trace=”none”, Colv=F)

However, this depends on knowing ahead of time your genes of interest.  It is not practical to generate a heatmap with hundreds or thousands of DE genes.

I wanted to produce something approximating a volcano plot for EBSeq results.  What I came up with initially was the following:

To make this plot, I had to grab some data arrays from the large object “EBOut” that is produced by calling the “EBTest” method and from the “GeneFC” object as below:

plot(GeneFC$PostFC, EBOut$PPDE, 
xlim =c(0,5), ylim=c(0,1), 
main="Control/Experimental FC vs. PPDE",
sub=GeneFC$Direction, xlab="EBSeq Posterior Fold Change", ylab="EBSeq posterior prob of DE")

abline(h=0.95)

The “abline” command places a horizontal line where the PPDE is equal to or greater than 95%.  This would be equivalent to an FDR of 0.05.

If you want to inspect the plot interactively in R to identify gene names above the threshold and/or with large posterior fold changes you would use:

identify(GeneFC$PostFC, EBOut$PPDE, labels=names(GeneFC$PostFC))

To make it look more like a canonical volcano plot, I then tried:

plot(log2(GeneFC$RealFC), EBOut$PPDE, 
xlim =c(-5,5), 
ylim=c(0,1), 
main="Log2FoldChange vs. PPDE", 
xlab="EBSeq Log2 Fold Change", ylab="EBSeq PPDE")

Creating the following plot:

This is good, except I want to subset the data and add colors. To do this I need to create a new dataframe from the EBOut$PPDE and GeneFC$PostFC objects:

volc_df = data.frame(EBOut$PPDE, GeneFC$PostFC)

With everything in one dataframe, plotting and subsetting the data is easier. Inspired by this post at Stephen Turner’s “Getting Genetics Done” blog, I prepared my final colored volcano plot as follows:

with(volc_df, plot(log2(PostFC), PPDE, pch=20, main="Volcano Plot EBSeq", xlim=c(-5,5)))

abline(h=0.95)

with(subset(volc_df, PPDE > 0.95 & abs(log2(PostFC)) < 2), points(log2(PostFC), PPDE, pch=20, col="orange")) 

with(subset(volc_df, PPDE > 0.95 & abs(log2(PostFC)) < 2), points(log2(PostFC), PPDE, pch=20, col="red"))

The final plot looks like this: