GeneOverlap (version 1.8.0)

drawHeatmap: Visualize GeneOverlapMatrix objects as heatmaps

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

"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)