Data format to produces a heatmap like this

Question

[prp291]

Hi,

My question is simple. I am just not just that how to arrange my data matrix to produces a heatmap to show a disticnt band in each tissue (preferential expression) like Figure 4 of this article.

Thanks

[kumar.vinod81]

Try this for GUI....very good

http://www.hiv.lanl.gov/content/sequence/HEATMAP/heatmap_mainpage.html

Answer 1

[Alternative]

Try to play with different clustering algorithms (i.e ward, ...) and different scales and scale colors when drawing your heatmap. In their methods they say that they used heatmap.2 (R package).

Hint: by limiting the scale, you avoid outliers from messing up with your scale and heatmap colors.

[prp291]

I tried different clustering algorithm but none of them seems to work for me. Thanks though

[Jean-Karim Heriche]

Do you know that you have such a structure for your data ? If you know which tissue each row corresponds to, you can just reorder your matrix to group the rows by tissue. If there is a structure corresponding to tissues, it should become apparent (possibly with the proper scaling as Pierre suggested).