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Remove R script/notebook package installs from gene-set-enrichment and ATRT (Part 3 of N)
#703
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cansavvy
commented
May 21, 2020
| if (!("ComplexHeatmap" %in% installed.packages())) { | ||
| install.packages("ComplexHeatmap") | ||
| } | ||
| library(ComplexHeatmap) |
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I accidentally deleted this so I ended up adding in the necessary ComplexHeatmap:: bits.
cbethell
approved these changes
May 22, 2020
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LGTM 👍
It looks like the only file that changed here was analyses/molecular-subtyping-ATRT/plots/atrt_heatmap.png and it appears that it is only the color scheme of the plot that change.
That being said, the relevant script should probably be updated to use one of the color palettes in figures/palettes to set up color annotations for this plot, but that is beyond the scope of this PR.
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Purpose/implementation Section
What was your approach?
I'm removing R package installations in the scripts in accordance with #690
I'm keeping track of the PRs I file for that issue there.
Here I'm addressed
gene-set-enrichment-analysisandmolecular-subtyping-ATRTremoval of package installs and reruns.01-conduct-gsea-analysis.Rand re-ranrun-gsea.sh02-ATRT-molecular-subtyping-plotting.Rand01-ATRT-molecular-subtyping-data-prep.Rmdand re ranbash run-molecular-subtyping-ATRT.sh02-ATRT-molecular-subtyping-plotting.Radded someComplexHeatmap::Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Everything look okay? Results that should be there are there?
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Yes, but the results shouldn't really be different.
Reproducibility Checklist
No changes are needed here.