aspectHeatmap {ClassDiscovery}R Documentation

Heatmap with control over the aspect ratio

Description

This function replaces the heatmap function in the stats package with a function with additional features. First, the user can specify an aspect ratio instead of being forced to accept a square image even when the matrix is not square. Second, the user can overlay horizontal or vertical lines to mark out important regions.

Usage

aspectHeatmap(x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL, distfun = dist, hclustfun = hclust, reorderfun = function(d, w) reorder(d, w), add.expr, symm = FALSE, revC = identical(Colv, "Rowv"), scale = c("row", "column", "none"), na.rm = TRUE, margins = c(5, 5), ColSideColors, RowSideColors, cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 + 1/log10(nc), labRow = NULL, labCol = NULL, main = NULL, xlab = NULL, ylab = NULL, keep.dendro = FALSE, verbose = getOption("verbose"), hExp = 1, wExp = 1, vlines = NULL, hlines = NULL, lasCol = 2, ...)

Arguments

x See documentation for heatmap.
Rowv See documentation for heatmap.
Colv See documentation for heatmap.
distfun See documentation for heatmap.
hclustfun See documentation for heatmap.
reorderfun See documentation for heatmap.
add.expr See documentation for heatmap.
symm See documentation for heatmap.
revC See documentation for heatmap.
scale See documentation for heatmap.
na.rm See documentation for heatmap.
margins See documentation for heatmap.
ColSideColors See documentation for heatmap.
RowSideColors See documentation for heatmap.
cexRow See documentation for heatmap.
cexCol See documentation for heatmap.
labRow See documentation for heatmap.
labCol See documentation for heatmap.
main See documentation for heatmap.
xlab See documentation for heatmap.
ylab See documentation for heatmap.
keep.dendro See documentation for heatmap.
verbose See documentation for heatmap.
hExp Height expansion factor; default = 1.
wExp Width expansion factor; default = 1.
vlines Vector of positions at which to draw vertical lines.
hlines Vector of positions at which to draw horizontal lines.
lasCol Axis label style (las) for columns.
... Additional arguments passed along to the image command.

Details

The new arguments hExp and wExp are "expansion factors" for the height and width of the figure, respectively. They are used to alter the arguments passed to the layout function internally to heatmap.

The new arguments hlines and vlines are used to specify points at which horizontal or vertical lines, respectively, should be overlaid on the image.

Value

The same as the heatmap function.

Author(s)

Kevin R. Coombes <kcoombes@mdanderson.org>

See Also

heatmap

Examples

nC <- 30
nR <- 1000
fakeData <- matrix(rnorm(nC*nR), ncol=nC, nrow=nR)
aspectHeatmap(fakeData, scale='none', hExp=2, wExp=1.4, margins=c(6,3))
aspectHeatmap(fakeData, scale='none', hExp=2, wExp=1.4, margins=c(6,3), vlines=15.5, hlines=c(100, 300))

[Package ClassDiscovery version 1.3 Index]