[R] Heat map in R

lraeburn at sfu.ca lraeburn at sfu.ca
Wed Jan 5 22:33:55 CET 2011

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_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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