Chr instability: PR 2 of 3: Create binned count heatmaps

[cansavvy]

Purpose/implementation Section

The next 3 PRs are the redone versions of the material that was included in #492.

This first PR includes the second of three notebooks which contain the material that was originally all in the previous 01 notebook.

What scientific question is your analysis addressing?

The items on #487 pertaining to this PR:

• The excluded regions BED file needs to be used
  - For the denominator for calculating densities
  - For marking NA on heatmap

What was your approach?

This takes the binned counts from the 01-localization notebook and makes the heatmaps for them.

What GitHub issue does your pull request address?

#487

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

• Are you able to figure out why the colors for histologies are not staying consistent even though I actually specify them specifically?
• Should I make the color function key adjusted for each dataset? Or do we like the consistency across the heatmaps?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

The plots will be in the next two notebooks which I will add in the next two PRs.

What is your summary of the results?

Here's the rendered html: https://cansavvy.github.io/openpbta-notebook-concept/chromosomal-instability/02a-plot-chr-instability-heatmaps.nb.html

Reproducibility Checklist

These items were done previously.

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date (Note it includes documentation for the upcoming notebooks as well.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[cansavvy]

@jashapiro , do you have an outstanding concerns regarding this PR? Were your changes implemented as you expected?

[jashapiro]

Now that the heatmap is mostly what we want, this looks good to go in. Just the request to update docs of breaks_heatmap() to reflect some of the constraints on structure of the color list and histology data frame.