Visualization Of Overlapped Gene Sets

Question

[chae]

Hi, I am new to microarray analysis. In brief, I want to draw a matrix figure like Fig.3 of this paper http://www.intechopen.com/download/get/type/pdfs/id/24851.

I have 4 different different data sets (like AD,DS,HD,PD in Fig.3) and analyzed significant gene sets from GSEA based on KEGG, GO BP, REACTOME, and BIOCARTA. From the gene sets, I'd like to create overlap matrix like Fig 3a and hypergeometric test matrix like Fig3b. That is, variables of each data set is the name of gene set (ex. signal transmission).

Is there any R package/R command to draw these figures?

Answer 1

[Madelaine Gogol]

You could use image() and then text() , but keep in mind you may need to transform and reverse the row order to get it to look like your data frame. Also, you'll have to make the scale separately. Here's an example for the heatmap part... Or here's a messy script that I've used.

You could try pheatmap also.

Answer 2

[Charles Warden]

Seems similar to what you can produce with heatmap.2, except I don't typically see values on each cell (especially if aren't necessarily used for clustering/visualization, such as the p-values). It is an interesting alternative to the venn diagrams in Figure 2 (which I think you can produce using the vennerable package).

Perhaps it is some custom implementation of the default heatmap() package?

http://flowingdata.com/2010/01/21/how-to-make-a-heatmap-a-quick-and-easy-solution/