Hi I have constructed a pan-genome using reciprocal blast hits(RBH) of 5 species genome.As expected the pan-genome contains the core genes(shared/conserved in all species),partially shared genes (shared/conserved between two or more species but not all) and unique genes(found in single specie).Now I am trying to visualize the obtained distribution of genes(core,partially shared and unique) onto a heat map.I tried many freely available resources for generating heat map but most of them deal with displaying microarray/expression data therefore I request suggestions which deal in generating heat map of pan-genome. Thanks Robert
R is great for these sorts of visualizations. You won't have to learn too much. My preferred R gui is R Studio, which is great for novices.
This one seems very nice and straightforward: http://flowingdata.com/2010/01/21/how-to-make-a-heatmap-a-quick-and-easy-solution/
My leaning is for MeV for quick and dirty things, as Madelaine recommended. It's quick to get to the result, and offers some nice ways to reslice the data.
The most generic tool I can think of is... Excel. One can use the "Conditional Formatting" feature to select a table and paint it dynamically according to cell contents.
I imagine in your case you'd have one row per gene (sorted according to what? position in the human genome?) and one column per species. This would yield a very long matrix - perhaps not the most amenable to plotting as a heatmap, unless you break it into segments and lay these out side by side. Nevertheless, in Excel it will be trivial to make the columns wide enough, and by zooming the spreadsheet out you can get a reasonable heatmap very easily.
Conditional formatting is a bit clumsy in version 2008 of office, but by version 2011 it's actually quite powerful.