re-create 5D forest plot

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

With #1356 in, we had to re-create 5D forest plot

What was your approach?

rerun script

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)?

new FP

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

• [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.

[sjspielman]

The code here should also be updated, not just rerun. For example, see the term_order and term_labels variables in the script - Unknown/Unavailable should be removed from there.

In addition, I want to note that in this updated model, Macrophage 1 now has an estimate, but it's lower bound and upper bounds are -Inf and Inf respectively. I think we should continue to exclude this point from the figure, but describe in figure caption that it's coefficient is -8.951217e+04 with infinite CIs and P=0.99. Edit: Those numbers are from here

[jharenza]

Ahhh thanks for catching this. Will update as soon as I can!

[jharenza]

@sjspielman code/plot is updated

[jharenza]

One more change here and then I think we're good to go. The comments on lines 35-38 should be updated, since Macrophage M1 estimates/CIs have changed from the original model. We want to indicate in these comments it is NOT significant but has infinite CIs.

whoops, updated

[sjspielman]

This code does not run through CI so we can merge before checks complete.