plotHeatmap {yarn} | R Documentation

## 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)

[Package yarn version 1.12.0 Index]