sjspielman
commented
1 year ago @jaclyn-taroni I'm going to dismiss your review here and request a new one soon, since the code is wrong and we both missed it the first time!
In the new script I added here, the code currently reads in the "original" module result files: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/4c5a70e42de85d68d6e5897a2f0667ef5d1b2255/figures/scripts/figS7-tp53-telomerase-tumor-purity-threshold.R#L49-L53
And then filters down to relevant IDs from there: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/4c5a70e42de85d68d6e5897a2f0667ef5d1b2255/figures/scripts/figS7-tp53-telomerase-tumor-purity-threshold.R#L111-L112
That was wrong! I should be reading in the threshold result files in the first place, without needing to filter in this script. The files I should be reading in are as follows, and then inner_joining with hypermutators for point colors.
analyses/tp53_nf1_score/results/tumor-purity-threshold/tp53_altered_status_tumor-purity-threshold.tsvanalyses/telomerase-activity-prediction/results/TelomeraseScores_PTBAStranded_FPKM_thresholded.txt
Towards #1665
This PR takes additional steps to establish a tumor purity supp figure, which we're going to call S7.
figures/scripts/figS7-tp53-telomerase-tumor-purity-threshold.Rto make a boxplot+legend that matches main text Figure 4D. I realize in #1671 I did export a PDF of colorful violins, but since an EXTEND plot was still needed I just went for it here. I guess we won't need the colorful violins, but they don't hurt anyone just sitting there!figures/script: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/f924b025bfa02be5dec3c777c0641f6035553b01/figures/scripts/fig4-tp53-telomerase-panels.R#L248-L456figures/scripts/README.md, but indicated TBD which panel this is for nowsupp-subtype-umap-panels.R-> (figs6-subtype-umap-panels.R)figures/generate-figures.shto copy over previously-made panels and runfigures/scripts/figS7-tp53-telomerase-tumor-purity-threshold.R.After this PR, the final step towards completing #1665 is to compile panels. I'm thinking something like (and I'll find a place for the UMAP panel when I dive in?)