Generate plot/counts for the manuscript

zzgeng commented 1 month ago

Purpose/implementation Section

What scientific question is your analysis addressing?

What was your approach?

What GitHub issue does your pull request address?

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

Which areas should receive a particularly close look?

figures/manuscript_OPC/figure/ and figures/manuscript_OPC/ R markdowns

Is there anything that you want to discuss further?

The schematic will be updated.

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.

zzgeng commented 1 month ago

hi @zzgeng thanks for getting started on these! I was hoping we could more directly mirror the plots you had on your poster. Can you create the tumor descriptor plot as a piechart and then the experimental strategy by cohort as a stacked barplot, both of these by match_id perhaps (that would be number of unique tumors). Can you also use the figure theme we have in our repos (eg: https://github.com/d3b-center/pbta-splicing/blob/main/figures/theme_for_plots.R, you can pull this over). I like the colors on your poster, so we can stick with those or similar if you recall what was used. For experimental strategy, perhaps we can make a new annotation called labeling the cohorts as "Pediatric" or "Adult", and facet the plot by that thing (age_group?) That would put GTEX and TCGA in a second facet, and won't blow out the cohorts in Pediatric. Does that make sense?

Thank you for the advice! I have made changes based on the comments. However, I cannot find Gtex in cohort or subcohort column. I wonder if I was looking at the wrong column?

jharenza commented 1 month ago

hi @zzgeng thanks for getting started on these! I was hoping we could more directly mirror the plots you had on your poster. Can you create the tumor descriptor plot as a piechart and then the experimental strategy by cohort as a stacked barplot, both of these by match_id perhaps (that would be number of unique tumors). Can you also use the figure theme we have in our repos (eg: https://github.com/d3b-center/pbta-splicing/blob/main/figures/theme_for_plots.R, you can pull this over). I like the colors on your poster, so we can stick with those or similar if you recall what was used. For experimental strategy, perhaps we can make a new annotation called labeling the cohorts as "Pediatric" or "Adult", and facet the plot by that thing (age_group?) That would put GTEX and TCGA in a second facet, and won't blow out the cohorts in Pediatric. Does that make sense?

Thank you for the advice! I have made changes based on the comments. However, I cannot find Gtex in cohort or subcohort column. I wonder if I was looking at the wrong column?

It got filtered out, but I updated the code. I also ended up splitting the plots so there wasn't so much white space and created a paneled figure 1 with biorender, also committed here. I'll work on updates to the workflow today. Thanks so much!

jharenza commented 1 month ago

does not use GHA

d3b-center / OpenPedCan-analysis