On Jun 30, 2011, at 8:02 PM, Levi Waldron wrote:
I would like to draw horizontal or vertical lines on a heatmap to
highlight the clusters at some specified cut depth of the dendrogram.
As a hacked example, the following code would work if I could set the
coordinates of the top and bottom of the false color image correctly
(ymin and ymax), but the correct values seem to depend on the output
device and its size. I realize that heatmaps use a 2x2 layout which
makes the coordinate system non-obvious, but the result seems very
difficult to customize. I would appreciate any suggestions for manual
or pre-made solutions.
The code discloses the color image is made with the 'image' function
and that its arguments include:
..., xlim = 0.5 + c(0, nc), ylim = 0.5 + c(0, nr), ...
?image # for details of coordinate choices.
Given the way the coordinate systems of that call might get messed
up by the subsequent 'plot' call, my guess is that the fastest way to
get what you want is to hack 'heatmap' by adding a couple of argument
and sticking a couple of "highlighting" functions just after the image
call. (You haven't said how you are picking these levels.)
--
David.
Example:
set.seed(2)
x <- matrix(rnorm(1000),ncol=10) #obviously no real clusters here...
row.hclust <- hclust(dist(x))
row.dendro <- as.dendrogram(row.hclust)
heatmap(x,
Rowv=row.dendro)
row.cut <- cutree(row.hclust,3)[row.hclust$order]
cutpoints <- which(row.cut[-1]!=row.cut[-length(row.cut)])
ymin <- par("usr")[3] #in general incorrect
ymax <- par("usr")[4] #in general incorrect
for (i in cutpoints){
thisy <- ymin + (ymax-ymin)*(i-1)/nrow(x)
abline(h=thisy,lw=3)
}
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David Winsemius, MD
West Hartford, CT
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
