Plot heatmap of most variable genes

This function plots a heatmap of the gene expressions forthe "n" features of interest.

Usage

plotHeatmap(obj, n = NULL, fun = stats::sd, normalized = TRUE, log = TRUE, ...)

Arguments

obj

ExpressionSet object or objrix.

n

Number of features to make use of in plotting heatmap.

fun

Function to sort genes by, default sd.

normalized

TRUE / FALSE, use the normalized matrix or raw counts.

log

TRUE/FALSE log2-transform raw counts.

...

Additional plot arguments for heatmap.2.

Value

coordinates

Examples

data(skin)
tissues <- pData(skin)$SMTSD
plotHeatmap(skin,normalized=FALSE,log=TRUE,trace="none",n=10)
# Even prettier
# \donttest{
# library(RColorBrewer)
data(skin)
tissues <- pData(skin)$SMTSD
heatmapColColors <- brewer.pal(12,"Set3")[as.integer(factor(tissues))]
heatmapCols <- colorRampPalette(brewer.pal(9, "RdBu"))(50)
plotHeatmap(skin,normalized=FALSE,log=TRUE,trace="none",n=10,
 col = heatmapCols,ColSideColors = heatmapColColors,cexRow = 0.6,cexCol = 0.6)
# }