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

[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.

Thanks