drawHeatmap {GeneOverlap} | R Documentation |
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)