[BiO BB] How to make a plot of phylogenetic profile?

[Leonardo Martins]

As spoken by Sarah Wang:
> Hi, 
> 
> Can anybody give me a hint of how to do this:
> I want to make a plot -- heat map like but without color gradient for
> phylogenetic  profile. I've seen these plots in publications but don't know
> how to make one. 
> What I want is for example, the columns are 100 genes (orthologs, only one
> best hit for one species), the rows are 100 species, if an ortholog exist in
> for a gene in a species, the corresponding cell is shaded.
> I use R and Perl but not Matlab.

  I believe that, in R, the function "heatmap()" will do the trick. If your data 
is a matrix with 0's and 1's, then you can try
 > heatmap (mydata, col=c("white","black"), scale="none")
 (where the option "scale" is redundant, but will prevent the normal
standardization of the rows). If you don't need the dendrogram produced, 
just add the options "Colv=NA" and "Rowv=NA". Or you may use the underlying 
"image()" function.

  Sincerely,
      Leo

-- 
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Leonardo de Oliveira Martins 
Mobile: 080-3395-6334
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Biometrics Laboratory at the University of Tokyo, Japan
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