[R] Heat map in R
juliet.hannah at gmail.com
Sun Jan 9 16:10:49 CET 2011
Make sure your data is a matrix. There are many examples of expression heatmaps
available on the bioconductor list. After checking out these examples, I would
post to the bioconductor list if you are still having problems. Also
consider a small
example to get you a working heatpmap. You have to install two
bioconductor packages for this by using:
This will also install other bioconductor packages that are needed.
# just creating create data
bcell <- grep("^B", as.character(ALL$BT))
types <- c("NEG", "BCR/ABL")
mysub <- which(as.character(ALL$mol.biol) %in% types)
bc <- ALL[, intersect(bcell, mysub)]
bc$BT <- factor(bc$BT)
bc$mol.biol <- factor(bc$mol.biol)
filter_bc <- nsFilter(bc,var.cutoff=0.9)
myfilt <- filter_bc$eset
e <- exprs(myfilt)
# end of data creation
# 880 79
#  "matrix"
On Wed, Jan 5, 2011 at 4:33 PM, lraeburn at sfu.ca <lraeburn at sfu.ca> wrote:
> 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!
> View this message in context: http://r.789695.n4.nabble.com/Heat-map-in-R-tp3176478p3176478.html
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