update MB immune cell FP - 5d

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

update immune cell FP for medulloblastoma per #1344 (staggered on #1344)

What was your approach?

added extent of tumor resection terms, reran code

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?

NA

Is there anything that you want to discuss further?

No

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)?

What is your summary of the results?

same as before- results are still significant even accounting for extent of tumor resection

Reproducibility Checklist

• [ ] 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.
• [ ] 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.

[jharenza]

@sjspielman something weird is happening - I added a grey color for the reference (we may want darker), and it is showing up, for ex, if I print forest_plot in line 142, but it is not coming up in the final PDF. Not sure why. Also, do you think grey is sufficient or do you want to also change shape? Would you go about the latter by adding a shape column in the survival_df?

[sjspielman]

I went ahead and added some commits here to fix the gray point appearing, and some similar changes to what I did in #1346.

I think the gray alone looks totally fine, and changing shape also would be excessive visual noise. The figure looks good to me at this point and code doesn't require CI, so in the interest of time I'm going to merge.