What scientific question is your analysis addressing?
From issue #1267, this PR adds more organization to the figures/pdfs/supp directory.
What was your approach?
Updated figures/README.md to explain this organization
Added two undocumented supplementary figure scripts to the figures/scripts/README.md
Updated relevant scripts to export figures to appropriate directory, and moved figures accordingly
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Should I change new directory names to, for example, pdfs/supp/figS3 instead of pdfs/supp/fig3 to be even clearer these directories are supp?
There is one script in figures/scripts/TelomeraseActivities.R that exports some supplementary figures, but not clear which supplementary figure(s) or panel(s) these will go into. That said, it also doesn't appear as though this script has been run and actually generated figures in these directories. My sense is this script will be substantially updated (maybe entirely rewritten) when these figures are solidified, since the main text figures for telomerase activity have to be updated too. For now I am leaving this file alone, in favor of future issues which will deal with telomerase activities.
There is also the directory pdfs/supp/sample-distribution/. Should that be somewhere in particular?
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Yes
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
[x] This analysis module has a README and it is up to date.
[x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
[x] The analytical code is documented and contains comments.
Purpose/implementation Section
What scientific question is your analysis addressing?
From issue #1267, this PR adds more organization to the
figures/pdfs/suppdirectory.What was your approach?
figures/README.mdto explain this organizationfigures/scripts/README.mdDirections for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
pdfs/supp/figS3instead ofpdfs/supp/fig3to be even clearer these directories are supp?figures/scripts/TelomeraseActivities.Rthat exports some supplementary figures, but not clear which supplementary figure(s) or panel(s) these will go into. That said, it also doesn't appear as though this script has been run and actually generated figures in these directories. My sense is this script will be substantially updated (maybe entirely rewritten) when these figures are solidified, since the main text figures for telomerase activity have to be updated too. For now I am leaving this file alone, in favor of future issues which will deal with telomerase activities.pdfs/supp/sample-distribution/. Should that be somewhere in particular?Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Yes
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.