Hi again :)

I want to plot a heatmap of all contrasted sites, not just the ones identified as DB.

I've used this code:

dba.plotHeatmap(cont_ME, contrast=1,
                                th = 1,
                                correlations=FALSE)

How is the sorting done? I see only X top sites, but don't know what default sorting was done to give these top sites. the sortFun parameter is said to be "Only relevant when using global binding matrix"

Thanks!

Michal

Analyzed sites are sorted by FDR (lowest first). Only the first maxSites sites are used, so if you want to show more sites, you can increase this from its default value of maxSites=1000. It gets slow if too many sites are added, but you can speed things up by eliminate the site (row) dendrogram by setting dendrogram="column" (default is "both"). The sites will then be shown with the ones most confidently identified as being differentially bound on top. You can always assign the return value of a call to dba.plotHeatmap() to a variable, which is a GRanges object containing the sites in the heatmap in the order they are plotted (returned "invisibly").