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CN Status Heatmap (PR 2 of 2) #603

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May 15, 2020
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97da925
The basic set up is there. Needs more work
cansavvy Mar 3, 2020
73b6292
Push this version of the heatmap though its gonna change
cansavvy Mar 4, 2020
99bd2d5
Sort of working
cansavvy Mar 4, 2020
29aa5d9
Merge remote-tracking branch 'origin/cn-status-heatmap' into cn-statu…
cansavvy Mar 4, 2020
f441b27
Neatened up things
cansavvy Mar 4, 2020
dd63b5f
Sorted out a few error handling items
cansavvy Mar 4, 2020
574a75e
Almost there
cansavvy Mar 4, 2020
f16075a
It's working. Needs more documentation and tweaks
cansavvy Mar 4, 2020
73c9c7d
documentation!!
cansavvy Mar 4, 2020
ebba0d7
Organize and make functions in their own util folder
cansavvy Mar 4, 2020
0b1219c
Add length filter and fix error
cansavvy Mar 4, 2020
1791b6d
Merge branch 'cn-status-heatmap-1' into cn-status-heatmap
cansavvy Mar 4, 2020
cf93927
Refreshy the notebook
cansavvy Mar 4, 2020
9b71c3e
Merge branch 'cn-status-heatmap' into cn-status-heatmap-1
cansavvy Mar 4, 2020
6b69b8e
Add to CircleCI
cansavvy Mar 4, 2020
dfec47c
Merge branch 'cn-status-heatmap' into cn-status-heatmap-1
cansavvy Mar 4, 2020
2c9d4dd
Streamline the PR to functions and README
cansavvy Mar 4, 2020
1a9b4dc
Minor updates to READMEs
cansavvy Mar 4, 2020
80ddd77
Update some minor comments and etc.
cansavvy Mar 4, 2020
9f0b086
Merge branch 'master' into cn-status-heatmap-1
cansavvy Mar 4, 2020
2709999
Merge remote-tracking branch 'upstream/master' into cn-status-heatmap-1
cansavvy Mar 4, 2020
9927c61
Merge remote-tracking branch 'origin/cn-status-heatmap-1' into cn-sta…
cansavvy Mar 4, 2020
a34cddd
Merge branch 'master' into cn-status-heatmap
cansavvy Mar 4, 2020
691cb10
extra space in config file
cansavvy Mar 4, 2020
95693cc
extra space in config file
cansavvy Mar 4, 2020
09f166c
fix a minor error.
cansavvy Mar 4, 2020
3c16dc7
Forgot this should not be in CI until next PR
cansavvy Mar 5, 2020
c735a62
refreshing notebook
cansavvy Mar 5, 2020
06333b0
Found some of the indexing problems I was having
cansavvy Mar 5, 2020
277848a
Merge branch 'master' into cn-status-heatmap
cansavvy Mar 5, 2020
a12cc90
Fix indices thing
cansavvy Mar 5, 2020
ab541c7
Merge branch 'master' into cn-status-heatmap-1
cansavvy Mar 5, 2020
4edf747
Use 10Mb cutoff and refresh notebook
cansavvy Mar 5, 2020
9b41ca7
Merge remote-tracking branch 'origin/cn-status-heatmap' into cn-statu…
cansavvy Mar 5, 2020
f95e4d8
Edit some comments
cansavvy Mar 5, 2020
c6eb52b
Merge branch 'master' into cn-status-heatmap-1
cansavvy Mar 9, 2020
48f209b
Merge branch 'master' into cn-status-heatmap
cansavvy Mar 9, 2020
cd3cdd4
Merge branch 'master' into cn-status-heatmap-1
cansavvy Mar 11, 2020
0ed90e0
Merge branch 'master' into cn-status-heatmap
cansavvy Mar 11, 2020
69db550
Merge branch 'master' into cn-status-heatmap
cansavvy Mar 19, 2020
a5691d0
Merge branch 'master' into cn-status-heatmap-1
jaclyn-taroni Mar 26, 2020
0e737f2
Merge branch 'master' into cn-status-heatmap-1
cansavvy Mar 27, 2020
a2a2c7f
Merge branch 'master' into cn-status-heatmap
cansavvy Mar 27, 2020
5eca2fb
Some typo fixes
cansavvy Mar 27, 2020
2e367bf
Update to unified color palette
cansavvy Mar 27, 2020
1a6b505
Fix some of the annotation objs and refresh
cansavvy Mar 27, 2020
6cf212f
Merge branch 'master' into cn-status-heatmap-1
jaclyn-taroni Mar 30, 2020
f74a4dd
Incorporate @cbethell 's suggestions
cansavvy Mar 31, 2020
f2b2fe7
Merge branch 'master' into cn-status-heatmap-1
jaclyn-taroni Mar 31, 2020
53632a1
Use @jaclyn-taroni 's wording suggestions
cansavvy Mar 31, 2020
cf8fa2b
Merge branch 'master' into cn-status-heatmap-1
cansavvy Mar 31, 2020
d16c1dc
Incorporate @cbethell 's suggestions
cansavvy Apr 1, 2020
05d2e82
Add more details about `bp_per_bin` in the README
cansavvy Apr 1, 2020
8216be9
Merge branch 'master' into cn-status-heatmap-1
cansavvy Apr 1, 2020
4922503
Merge branch 'master' into cn-status-heatmap
cansavvy Apr 8, 2020
4651676
Incorporate @jashapiro suggestions
cansavvy Apr 8, 2020
9258b57
Merge branch 'cn-status-heatmap-1' into cn-status-heatmap
cansavvy Apr 8, 2020
7ff5b10
Update CN heatmap with the other PR changes
cansavvy Apr 8, 2020
3e2df17
Merge branch 'master' into cn-status-heatmap-1
cansavvy Apr 8, 2020
181d269
Reformat that last logic bit with the uncallables
cansavvy Apr 8, 2020
a4c249a
Refresh the notebook
cansavvy Apr 8, 2020
718e4e9
Make updates to the logic and its handling of uncallables
cansavvy Apr 8, 2020
6e39d01
Forgot to take out development things.
cansavvy Apr 8, 2020
a46e3bd
Get rid of dev thing and refresh the notebook
cansavvy Apr 8, 2020
e4aa934
Use @josh logic
cansavvy Apr 8, 2020
f9f812a
Comment updates
jashapiro Apr 10, 2020
43e9825
Merge branch 'cn-status-heatmap-1' into cn-status-heatmap
cansavvy Apr 10, 2020
53fe78d
It's not right, but its less wrong: samples are in right order
cansavvy Apr 10, 2020
054a059
Merge branch 'master' into cn-status-heatmap
cansavvy Apr 13, 2020
df23c14
Resolve reordering error
cansavvy Apr 13, 2020
af29757
Merge remote-tracking branch 'cansavvy/cn-status-heatmap' into cn-sta…
cansavvy Apr 13, 2020
fe9b404
Switch logic so `neutral` is default.
cansavvy Apr 13, 2020
2321c24
Incorporate @cbethell 's suggestions
cansavvy Apr 20, 2020
43fbcd1
Merge branch 'master' into cn-status-heatmap
cansavvy Apr 20, 2020
6fb86c9
Heatmap legend is in right spot but not horizontal
cansavvy May 12, 2020
b999962
Horizontal Legend!!!
cansavvy May 12, 2020
9226a78
linter it
cansavvy May 14, 2020
7681562
Merge branch 'master' into cn-status-heatmap
jashapiro May 15, 2020
3d0172b
Docs clarifications on thresholds and change chr back to original colors
cansavvy May 15, 2020
0ec01d5
Merge branch 'master' into cn-status-heatmap
cansavvy May 15, 2020
d2051a2
Up the resolution
cansavvy May 15, 2020
8bbc84c
Merge branch 'master' into cn-status-heatmap
jashapiro May 15, 2020
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4 changes: 4 additions & 0 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -163,6 +163,10 @@ jobs:
name: GISTIC Plots
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/gistic_plot.Rmd', clean = TRUE)"

- run:
name: CN Status Heatmap
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/cn_status_heatmap.Rmd', clean = TRUE)"

- run:
name: Gene set enrichment analysis to generate GSVA scores
command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash "analyses/gene-set-enrichment-analysis/run-gsea.sh"
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