plotHeatmap: Plot heatmap of most variable genes

In QuackenbushLab/yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Plot heatmap of most variable genes

Description

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

# 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)

QuackenbushLab/yarn documentation built on March 7, 2024, 3:53 p.m.