Hello,
I am trying to make a heatmap in R and am having some trouble. I am very new
to the world of R, but have been told that what I am trying to do should be
possible. I want to make a heat map that looks like a gene expression
heatmap (see http://en.wikipedia.org/wiki/Heat_map).
I have 43 samples and 900 genes (yes I know this will be a huge map). I also
have copy numbers associated with each gene/sample and need these to be
represented as the colour intensities on the heat map. There are multiple
genes per sample with different copy numbers. I think my trouble may be how
I am setting up my data frame.
My data frame was created in excel as a tab deliminated text file:
Gene Copy Number Sample ID
A 1935 01
B 2057 01
C 2184 02
D 1498 03
E 2294 03
F 2485 03
G 1560 04
H 3759 04
I 2792 05
J 7081 05
K 1922 06
. . .
. . .
. . .
ZZZ 1354 43
My code in R is something like this:
data<-read.table("/Users/jsmt/desktop/test.txt",header=T)
data_matrix<-data.matrix(data)
data_heatmap <- heatmap(data_matrix, Rowv=NA, Colv=NA, col = cm.colors(256),
scale="column", margins=c(5,10))
I end up getting a heat map split into 3 columns: sample, depth, gene and
the colours are just in big blocks that don't mean anything.
Can anyone help me with my dataframe or my R code? Again, I am fairly new
to R, so if you can help, please give me very detailed help :)
Thanks in advance!
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