I have a very simple question, which I couldn't find an answer after surfing the web. I'd appreciate if someone can link the answer, if it's already there.

After successfully generating plot.profile, I found that the y-axis in the graph doesn't have any description (Red circle at the top). If I report dba object used for the plot.profile (thatis, dba.report(dbaobject)), there are numeric values for each genotype/cell type. But what are they? Read counts? Scores?

Also, can I extract values of heatmap or I can mark gene names of certain heat map lines? For example, in the red circle on the BT474_Reistant heat map, I want to know which gene/locus it is by extracting the eigen value of heatmap or can I somehow label that specific heatmap element (the circled one)? I think this is related to profileplyr, but no luck to find a way to mark individual element.

Thank you in advance.

The numbers at the top are mean normalized read counts.

I don't know of a clean way to label a single site. However, using the sites parameter to dba.plotProfile(), you could specify the site as its own group with its own label (and color). In that case you'd probably want to specify groups for sites as a GRangesList.