Enhancer plot

[katosh]

This is PR draft comes with code and notebook for the enhancer plot.

There are some ToDos for enhancer_plot.ipynb before we merge:

• Replace example data
  The notebook currently uses data that is local to our compute cluster and that was produced before geneTF existed. Is there geneTF data we could use instead?
• Remove rpy2 dependency
  If the new data is in a different format we might not have to use rpy2 and certainly not the module R/4.0.0-foss-2019b.
• Simplify preprocessing
  Depending on the format of the new example data the preprocessing can be simplified.
• More documentation/explanation in notebook
  There is no explanation of what the plots show exactly so far.

These are just the most imminent changes that come to mind.

[jordanc17]

I've already removed the r2py dependency in the version I've been using for the figures, so I will update that and will work on the other tasks!

[katosh]

Thank you @jordance71. The version you pushed does not work for me though since it uses density_analysis that has not been pushed yet. Also the new plots seem broken and show errors. Do the dorc_peak_deltas actually contain arrays of floating point values?

[jordanc17]

@katosh it is still in progress. I wanted to make a commit locally with the changes I made so I could roll back changes easily as I'm trying to fix it but it got pushed when I pushed commits on another branch of the repository, I think.

[jordanc17]

• prevent plotting of genes with no associated peaks

[katosh]

Plotting genes without peaks is intentional. If you do not want them to be plotted you can set the min_peaks parameter to 1 (it defaults to 0).

[katosh]

I noted that the PR contains some log files in the directory logs/ and test-logs/ which might not be intentional.