Visualization

By default, GenomeRunner outputs n x m matrix of -log10 transformed p-values. n (rows) are genomic features (GFs) and m (columns) are features of interest (FOIs). Each cell shows enriched association (or depletion, if "-" is present) of a FOI with a GF. Such matrix is outputted into a tab-separated file "*_ChiSquare_Matrix.gr", which can be opened in Excel or any text editor.

How to visualize it? I have commented and elaborated on this before, and provided an R script for visualizing such a matrix. But what about those who are not familiar with R? Thanks to an excellent heatmap visualization tool, you can upload GenomeRunner' matrix to it, click "Submit", and voila! High quality PDF heatmap is ready. Also, it provides lots of ways for tweaking colors, clustering parameters (although default settings work OK). And it gives an R code to make such a heatmap, for your learning and use. So, head on to the heatmap visualization tool and try it out.