rerun immune-deconv with v15

[komalsrathi]

Purpose/implementation Section

What scientific question is your analysis addressing?

Rerun immune-deconv module on updated Dockerfile and v15

What was your approach?

• Removed features with 0 values across all samples before deconvolution. I have tested and it doesn't make any difference in the output but rather reduces the feature size.

• Fixed some color annotation.

What GitHub issue does your pull request address?

#543

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

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

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

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

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]

thanks so much for updating and running @komalsrathi . Can we just remove the plot script and plots- doing by cohort is not very informative and if we need plots for projects, they can be done in project specific repos. Thanks :)

[jharenza]

Going to merge this, since it reran successfully. Note, I commented out quantiseq. It ran in ~2 hours on EC2, but maybe we do not need to be running it since xcell has more cell types anyway.