cd06-0-aspectHeatmap: Heatmap with control over the aspect ratio

In ClassDiscovery: Classes and Methods for "Class Discovery" with Microarrays or Proteomics

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 is 1)
wExp	width expansion factor (default is 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 [e-mail]

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))

Example output

Loading required package: cluster
Loading required package: oompaBase

ClassDiscovery documentation built on Aug. 4, 2021, 3 p.m.