update tp53/telomerase forest plot(s)

jharenza commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Here, I update the tp53/telomerase forest plots to include extent of tumor resection. In addition, I am adding a second forest plot which has a term for LGG group. This is staggered on #1342

What was your approach?

Just updated the plots based on analysis in #1342

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?

I think that we should make the LGG plot now 4F, given the control for LGG. I do think the HGG plot is meaningful since the TP53 scores were not as predictive for HGG (except in DMGs, in which there is a significant hazard - goes along with what we are now learning via the PNOC paper/the subtyping forest plot we will add in 4G), and we can possibly add it to S4 as panel D (may have to landscape that figure). Thoughts on putting the hgg forest plot in S4?

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?

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

[ ] 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.
[x] The analytical code is documented and contains comments.

sjspielman commented 2 years ago

I added a few small commits here to fix the cut off x-axis and remove some hardcoding for ref levels.

This looks ready to me, but we should decide about the panel location before merging (since the code may need to be in a different script). I'm not sure what exactly is meant by "LGG plot" vs "HGG plot" since the model contains both LGG and HGG? There is only 1 plot here.

jharenza commented 2 years ago

I added a few small commits here to fix the cut off x-axis and remove some hardcoding for ref levels. 👍 This looks ready to me, but we should decide about the panel location before merging (since the code may need to be in a different script). I have this as 4F with HGG subtypes FP as 4G, then KM curve as 4H

I'm not sure what exactly is meant by "LGG plot" vs "HGG plot" since the model contains both LGG and HGG? There is only 1 plot here. This needs to be updated

jharenza commented 2 years ago

closing in favor of #1354

AlexsLemonade / OpenPBTA-analysis