Y axis PlotHeatMap Deeptools

Question

[fusion.slope]

Hello,

am wondering what values are represented in the Y axis of plotHeatMap in Deeptools.If we consider the first picture here:

http://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html

What are the values in the Yaxis on top left (on the box) and what are the values on the right along the heatMap? Do they represent the same thing?

Thanks in advance for any reply. Best

Answer 1

[Devon Ryan]

The values on the Y axis are whatever are in the bigWig files. If those files represent "alignment depth", then that's what's shown. If those files instead represent something like "1x normalized depth" or "depth vs. control" or "methylation percent" then that's what's depicted. computeMatrix only summarizes what's in one or more bigWig files, what you put in those files is then up to you.

[fusion.slope]

Thanks Devon, the fact is that am seeing that in my Plot the numbers do not correspond..

https://ibb.co/huvoJJ

Can you see it? Thanks in advance for any comment

[Devon Ryan]

The plot is an average over the columns of the heatmap. Perhaps the values look lower than you expected from the heatmap, but this is an artefact of interpolation and our generally bad ability as humans to eye-ball that sort of average exactly.

[sutturka]

This explanation helps. I have additional question:

What does negative scale imply on profile plot? I am plotting RNASeq data in two ways:

• Separate BAMs for control and treatment
• After BAMcompare i.e. after normalizing the treatment against control.

See image here.

Does negative value simply imply the signal is high in control than treatment?

[Devon Ryan]

The output of bamCompare was likely the log2 ratio, so negative values are regions where control is higher than treatment (assuming you did treatment vs. control rather than control vs. treatment).