Add cancer group plot to immune deconv notebook

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

Given that we are not highlighting any subtype-based immune cell type effects on survival, I think we should move the immune cell subtype plot to the supplement and create a cancer group plot as the main figure. This can go along with the GSVA immune scores, as I am discussing in the incoming PR for figure 5 updates in the manuscript repo.

Update - manuscript repo ticket draft here.

What was your approach?

• I added DMG as a subtype of interest, so that plot is updated
• I added a cancer group plot. This isn't as pretty as the mutational signatures plot, so needs some tweaking - please help @sjspielman :)

What GitHub issue does your pull request address?

NA

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

Which areas should receive a particularly close look?

I filtered cancer group > 15 to get the same subset as in mut sigs. I do slightly worry about two very similar plots, but they are showing completely different data, so I think we can go with it, unless you have any other ideas @sjspielman or @jaclyn-taroni ?

Is there anything that you want to discuss further?

• I think we may still add an HR plot or two for immune cells within cancer group to Fig 5, but I will need some more time after #1264 is completed to dig into the literature to determine what makes the most sense to show.
• I put this on the same y-scale because I thought it would be easier to talk pan-tumor, but I suppose that isn't entirely necessary and we can update this to be free-y. Thoughts?

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

yes

Results

What types of results are included (e.g., table, figure)?

new figures - updated subtype figure containing DMG and new cancer group figure

What is your summary of the results?

I am showing this by cancer group rather than immune cell type because I am talking about immune cells relative to others within a cancer group.

Reproducibility Checklist

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

Documentation Checklist

• [x] This analysis module has a README and it is up to date.
• [x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [x] The analytical code is documented and contains comments.

[jaclyn-taroni]

I'll review this!

[jharenza]

thanks @jaclyn-taroni - took the suggestions!