This PR is a bit large and contains all S7 panels, since I couldn't help myself what with the branch name... But, all exports are very straightforward!
This figure has not yet been re-compiled (3 new panels are being added during this round of revisions), but here is the previous compilation. The current panels you see are getting scooted down to become D-I, and new panels are A-C.
Here's the inventory. ⚠️ indicates that the code is in analyses/ modules, and therefore copying was also added to table/zenodo-upload/. Nothing here is particularly tricky, so I have very few notes!
I also learned that it seems our tidyverse version does not give you everything() and similar helpers just because you're calling them inside of dplyr::select() 😞
This is a barplot of counts, so I went ahead and just counted for them (since plot was made with geom_bar()). - Panel B: figures/scripts/figS7-UMAP-libraries.R
While I was here I also removed a ggplot argument show.legend = FALSE which apparently is not in our ggplot version, and it throws a warning during runtime and then does absolutely nothing in the plot. So, it's gone!
Let's take a second to check in overall here: What's left?
Panels for Figure S2 that need to be dealt with on AWS. This could get weird since data is HUGE, so we'll see if we can even put some of those files in github at all.
Panel S3A, which will be exported from from the tumor-purity-exploration module.
Oncoprint CSV files
Sample-level molecular alteration files associated with oncopints
Towards #1692.
This PR is a bit large and contains all S7 panels, since I couldn't help myself what with the branch name... But, all exports are very straightforward!
This figure has not yet been re-compiled (3 new panels are being added during this round of revisions), but here is the previous compilation. The current panels you see are getting scooted down to become D-I, and new panels are A-C.
Here's the inventory. ⚠️ indicates that the code is in
analyses/modules, and therefore copying was also added totable/zenodo-upload/. Nothing here is particularly tricky, so I have very few notes! I also learned that it seems our tidyverse version does not give youeverything()and similar helpers just because you're calling them inside ofdplyr::select()😞figures/scripts/figS7-seqcenter-barplot.Rgeom_bar()). - Panel B:figures/scripts/figS7-UMAP-libraries.Ranalyses/transcriptomic-dimension-reduction/04-explore-sequencing-center-effects.Rmdshow.legend = FALSEwhich apparently is not in our ggplot version, and it throws a warning during runtime and then does absolutely nothing in the plot. So, it's gone!analyses/tp53_nf1_score/10-tp53-tumor-purity-threshold.Rmdtp53_nf1_score/results/tumor-purity-threshold/selected relevant columns for each export.figures/scripts/figS7-tp53-telomerase-tumor-purity-threshold.Ranalyses/transcriptomic-dimension-reduction/06-umap-tumor-purity-threshold.Rmdanalyses/immune-deconv/03-quantiseq-at-threshold.RmdWhat to expect when you're expecting more PRs
Let's take a second to check in overall here: What's left?
tumor-purity-explorationmodule.