medullo cd274 expression/assess immune hot (figure 5E, S5J)

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

Adding a panel after the medullo forest plot to show the cd274 expression distributions across medulloblastoma subtypes.

What was your approach?

plot cd274 expression by mb subtype

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?

When plotting the cd8/cd4 ratios (advice from clinician Jess Foster), I opted to remove all Inf/NaN from the dataframe because all EPN had these values. Is that ok? We can put this in the supplement (S5-J) since I do mention in the text that many of these tumors are immune cold and this could be a good metric, even if rough.

Is there anything that you want to discuss further?

• Should we keep as boxplots or make violins?
• We need to add stats, but since nearly every pairwise stat is significant, I need some advice on this @sjspielman - should I just export the stat dataframe and write about them in the legend?

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)?

two new figures

What is your summary of the results?

• CD274 expression, even though low, is significantly different across MB subgroups. This has been previously reported with SHH and WNT having higher expression. We see the highest in WNT.
• We only see MB group 3 & 4 might be considered "immune hot" with a greater number of CD8+ vs CD4+ T cells. Most brain tumors are "immune cold" (also known, but we can show that we can use the quanTIseq fractions to estimate "hot" tumors which might be responsive to immune checkpoint blockade.

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 I think this is ready for re-review, but see my comment about the log scale plot

[jharenza]

@sjspielman changed the ratio plot back to linear scale, but this was not passing CI before - it holds up at line 608, but even if I add to not run that chunk in CI, still errors out. not sure why...

[sjspielman]

@jharenza I'm looking into this CI failure.

Edit - almost certainly because the param was not set up in the module script. Committing a change now to fix this.

[sjspielman]

This has passed CI so can be merged before the next round of checks are complete.