R: Heatmap with control over the aspect ratio

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>

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]