drawHeatmap: Visualize GeneOverlapMatrix objects as heatmaps

In GeneOverlap: Test and visualize gene overlaps

Description

Visualization function for GeneOverlapMatrix objects. Use color gradients to represent the odds ratios or Jaccard indices and the superimposed texts on the grids to represent the p-values of overlaps.

Usage

## S4 method for signature 'GeneOverlapMatrix'
drawHeatmap(object, 
    what=c("odds.ratio", "Jaccard"), log.scale=F, adj.p=F, cutoff=.05, 
    ncolused=9, grid.col=c("Greens", "Blues", "Greys", 
    "Oranges", "Purples", "Reds"), note.col="red")

Arguments

object	A GeneOverlapMatrix object.
what	What to plot? Odds ratio or Jaccard index.
log.scale	Whether log2 scale shall be used for odds ratios.
adj.p	Boolean label for whether p-values should be adjusted (using the Benjamin-Hochberg method) before showing.
cutoff	P-value cutoff to mask the insignificant comparisons.
ncolused	Number of colors used to represent the scale of odds ratios.
grid.col	Color for odds ratios.
note.col	Color for p-value texts.

Details

The grids that are below the p-value cutoff will be masked and shown as the lightest color.

Examples

data(GeneOverlap)
gom.obj <- newGOM(hESC.ChIPSeq.list, genome.size=gs.RNASeq)
drawHeatmap(gom.obj, adj.p=TRUE, cutoff=1,  # show all.
    ncolused=5, grid.col="Blues", note.col="black")
drawHeatmap(gom.obj, log.scale=TRUE, ncolused=5)
drawHeatmap(gom.obj, what="Jaccard", ncolused=5)

Example output

GeneOverlap documentation built on Nov. 8, 2020, 5:46 p.m.