drawHeatmap: Visualize GeneOverlapMatrix objects as heatmaps
In shenlab-sinai/geneoverlap-old: Test and visualize gene overlaps

Description Usage Arguments Details Examples

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.

## 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")

`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.

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

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)