Hi,
I am trying to create a heatmap with some specific requirements. Specifically,
I need to be able to center the color-scale around 0, and I need to truncate the
data so that a few extreme values do not cause the rest of the heatmap to appear
black (on a red/green scale).
After reading through and experimenting with heatmap, heatmap.2, heatmap_plus,
and heatmap_2, I believe heatmap.2 will provide the best solution - it appears
to be the only option that will center around 0 without me manually adjusting
the zlim. In addition, the color key and distributional information is useful
(at least for the non-truncated data).
Although I have not used truncated data at this point, I have so far been unable
to produce consistent dendrograms when I'm not producing the dendrogram as
part
of the heatmap. What am I missing?
###################################
R version 2.9.0 (2009-04-17)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
# The correct results> hv <- heatmap.2(x,
col=col.palette,
Colv=FALSE,
key=TRUE,
Rowv=cc1$order,
dendrogram="row",
scale="none",
tracecol="white",
cexCol=.5)
> hv$rowInd
[1] 26 23 5 19 15 4 2 16 21 13 22 12 10 20 7 3 25 1 8 11 24 9 18 14 17
[26] 6
# Attempt 1> cc = as.dendrogram(hclust(dist(x)))
> hv1 <- heatmap.2(x,
col=col.palette,
Rowv=cc,
Colv=FALSE,
key=TRUE,
dendrogram="row",
scale="none",
tracecol="white",
cexCol=.5)> hv1$rowInd
[1] 5 23 26 1 25 8 11 9 24 18 14 6 17 2 4 16 21 13 22 12 10 20 3 7 15
[26] 19
# Attempt 2> cutting <- cutree(hclust(dist(x)),k=8)
# I counted about 8 divisions in correct clustering> hv2 <- heatmap.2(x,
col=col.palette,
Rowv=cutting,
Colv=FALSE,
key=TRUE,
dendrogram="row",
scale="none",
tracecol="white",
cexCol=.5)> hv2$rowInd
[1] 5 23 26 1 25 8 11 9 24 18 14 6 17 15 19 2 4 16 21 13 22 3 7 12 10
[26] 20
# Attempt 3> correct.order <- hv$rowInd
> hv3 <- heatmap.2(x,
col=col.palette,
Rowv=correct.order,
Colv=FALSE,
key=TRUE,
dendrogram="row",
scale="none",
tracecol="white",
cexCol=.5)> hv3$rowInd
[1] 5 26 23 15 19 22 13 7 3 12 20 10 16 21 4 2 8 11 25 1 24 9 18 14 6
[26] 17
My understanding is that my first attempt is the same call heatmap.2 makes - so
there is no reason for the different results.
Note - if there is another way to create the heatmaps meeting my requirements
using other packages, that works too - I just need something to produce
consistent results.
Thanks!
Melissa Key
Graduate Student
Department of Statistics
Purdue University
