Dear R users, need help with my heatmap. I will really approciate some help.
Given the matrix:> head(x)
A B C D time
[1,] 0 8 0 0 1
[2,] 0 160 0 0 2
[3,] 0 175 0 0 3
[4,] 0 253 0 0 4
[5,] 79 212 0 0 5
[6,] 6 105 0 0 6
and call:
##------------ Heatmap --------------
library(RColorBrewer)
rc <- grey((nrow(x):1)/nrow(x))
heatmap(data.matrix(x[,1:4]), Rowv=NA, Colv=NA,
scale='none',labCol=NULL,
revC=TRUE, col = brewer.pal(9,'Greys'),
ylab='time',margins=c(6,5), cexRow=1.5, cexCol=1.5,
RowSideColors rc)
I end up with something like attached 'heatmap'.
How can I change my call to:
1) most important: there are black strips on the right-hand side, these are
the row numbers packed one on another. How to put there time points over,
say, 500 sec epochs (1,500, 1000...)
2) put a scale on the colour key on the left-hand side, and replace the
whole key on the right-hand side
3) have 'A'B'C'D' labels in horizontal orientation; replace
'time' label on
the left side
4) put frame around the plot
##----------------- Heatmap2 -----------------
I did not try with ggplot, but tried with 'heatmap.2':
heatmap.2(data.matrix(x[,1:4]), Rowv=NA, Colv=NA, dendrogram='none',
scale='none', labRow=FALSE, cexRow=1,cexCol=1,
col = brewer.pal(9,'Greys'), density.info='none',
key.size=1,
trace='none')
and got heatmap2 attached
if heatmap.2 is something you suggest, then the same questions apply + one
more:
5) how to change 'Color Key' label and put it along the rows
Best, robert
http://r.789695.n4.nabble.com/file/n3915575/heatmap.png
http://r.789695.n4.nabble.com/file/n3915575/heatmap2.png
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