Splitting up #921: Immune-deconv changes

[cansavvy]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR is a split off of #921 where I am updating the transcriptomic overview plot in response to the histology color palette table added in #898

This PR updates immune-deconv module to use the display group and hex codes of the palettes/histology_label_color_table.tsv table that is created by the notebook added in #899

What was your approach?

This PR updates one of the three modules that are ultimately used in the transcriptomic-overview plot that is ultimately updated in #921.

immune_deconv updates:

• analyses/immune-deconv/01-immune-deconv.R need to be updated to use display_group instead of short_histology.
• Also needed to update analyses/immune-deconv/02-summary-plots.R in the same way
• After these changes I re-ran OPENPBTA_DECONV_METHOD="mcp_counter" ./analyses/immune-deconv/run-immune-deconv.sh (The CIBERSORT.R Doesn't work unless you have that CIBERSORT.R script which we do not).

*Note that the palettes/histology_color_palette.tsv file itself is not deleted yet, I will do this in the last PR of this series (#927) so the other modules that use this file don't break in CI yet.

What GitHub issue does your pull request address?

Makes more progress toward addressing #898
Closes #926

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

• I ran it with the DECONV_METHOD used in circle CI and in the generate-figures script, but I notice there were originally plots for this method. Does this mean we don't really want this methods plots?
• I have more questions about why we are keeping CIBERSORT based methods since we can't re-run this (and haven't for almost a year). (We don't have access to the CIBERSORT.R script needed for this).

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

Yes?

Results

The results themselves don't really change here but will change in transcriptomic-overview.

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile. -- no new packages are needed.
• This analysis has been added to continuous integration.

Documentation Checklist

I checked the respective READMEs for these analyses and they did not require any updates for these changes.

• 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.

[cansavvy]

I didn't think this was relevant anymore so I deleted this step completely, but someone should let me know if something like this is still needed.

[jharenza]

confirmed this is ok to delete with the switch to harmonized dx

[cbethell]

The changes made to the scripts in this PR look good to me!

It appears that parts of the heatmap_MCPcounter.pdf and heatmap_xCell.pdf plots have been cutoff so the sizing will likely need to be adjusted.

As for your point in this PR's original comment:

I have more questions about why we are keeping CIBERSORT based methods since we can't re-run this (and haven't for almost a year). (We don't have access to the CIBERSORT.R script needed for this)

I also had the same question so I took a look at the README...

Per this module's README.md,

"We chose CIBERSORT (abs.) over MCP-Counter as it has the greatest number of overlapping immune cell types with that of xCell".

Also stated that,

"We recommend using MCP-Counter instead of CIBERSORT (abs.) when these files are not available to the user".

That said, I would argue that if this PR in particular goes in as is, we should update the README.md to reflect the change in method used.

[cansavvy]

Per this module's README.md,

"We chose CIBERSORT (abs.) over MCP-Counter as it has the greatest number of overlapping immune cell types with that of xCell".
"We recommend using MCP-Counter instead of CIBERSORT (abs.) when these files are not available to the user".

Yes. I saw these recommendations in the README. This is part of my question. Why are we keeping this around if it isn't something we can run? It might be something for a separate issue.

On the separate note, I did notice the plots are trimmed badly, I'll look into fixing that.

[cansavvy]

@cbethell , I tracked the CIBERSORT method issue mentioned above here: #931 and I fixed the plot margins. Let me know what you think.

[cbethell]

With issue #931 filed, this PR LGTM! 👍