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Chromosomal Instability (PR 3 of 3): The notebook with plots #419

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Jan 18, 2020
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Chromosomal Instability (PR 3 of 3): The notebook with plots #419

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a43dfd1
It's a start of a notebook
Jan 3, 2020
af29c7c
Got some of the code converted and working
Jan 3, 2020
89cfdee
Percent genome change plot added
Jan 3, 2020
226d906
Have overlap of CNV and SV
Jan 6, 2020
4b8871f
Breakpoint summary df
Jan 6, 2020
547117d
Got things mostly organized and the wrangling functions are formed up…
Jan 6, 2020
34fe36e
Load my functions as they are so far. TileGenome setting up
Jan 6, 2020
fce6e40
Made a plotting function that probably won't work yet
Jan 7, 2020
7fd1d28
Things are here, just need to test things, reorg and add more doc
Jan 7, 2020
e4b14f8
Plotting function works
Jan 7, 2020
35c908c
Merge remote-tracking branch 'upstream/master' into cin_setup
Jan 7, 2020
9f800d8
Merge remote-tracking branch 'upstream/master' into cin_setup
Jan 7, 2020
d3ee47d
It's working!
Jan 7, 2020
cc4e07a
Plots are working just need more doc
Jan 7, 2020
19c611e
Add a README and change the function file name
Jan 7, 2020
f4c2c6b
Some reorganization and adding the plots
Jan 8, 2020
0d9bf6c
lintered and neatened up some things
Jan 8, 2020
4ed2a25
Few more touches to the README
Jan 8, 2020
2d59523
Add the functions
Jan 8, 2020
6951c98
Edited a messed up comment
Jan 8, 2020
554c113
Merge branch 'master' into cin_functions
cansavvy Jan 8, 2020
9e0d321
Fixed some issues with the functions
cansavvy Jan 8, 2020
42d1f68
Add tumor type plots
Jan 8, 2020
454c70b
Rearrange and fix some things with the group calculations
Jan 8, 2020
ea3221b
Smoothing out some metadata handling of GenomicRanges
Jan 8, 2020
8c90043
Functions handle multiple samples
Jan 8, 2020
5a34518
The functions handle grouped data
Jan 8, 2020
0e7cbbb
Got rid of a development remnant I found
Jan 8, 2020
94560da
minor typo fixes
Jan 8, 2020
ce94432
Apply percentage filter to CNV data
Jan 8, 2020
39623c8
Minor edits
Jan 9, 2020
d042a68
Changes to logic and plot names
Jan 9, 2020
252884f
Incorporate @sjspielman suggestions
Jan 9, 2020
1a95792
Missed a paranthesis
Jan 9, 2020
b0f9cb9
re-linter
Jan 9, 2020
8095c4e
Merge branch 'cin_functions' into cin_setup
Jan 9, 2020
138638d
Reorganize the plots
Jan 9, 2020
a4ee467
Add tumor type plots
Jan 9, 2020
e0d9d92
Add to CircleCI
Jan 9, 2020
8b48203
Merge branch 'master' into cin_setup
cansavvy Jan 9, 2020
2fa662f
Get rid of development remnant
Jan 9, 2020
8b61db3
Merge remote-tracking branch 'origin/cin_setup' into cin_setup
Jan 9, 2020
1e2614e
Delete sample PNGs and zip up tumor type PNGs
Jan 9, 2020
2b42ee1
some svcnvplus files snuck in.
Jan 9, 2020
c6f3fc2
Fix tumor-type plots and add automatic zip
Jan 9, 2020
d6a53c9
Get rid of 01-process-sv-file.R source step. Use straight file.
Jan 9, 2020
96b1909
Had to change sample name getter step
Jan 9, 2020
e4582b4
Fix a missing `dplyr::`
Jan 9, 2020
13c17f5
Add chromosomal instability to main README table
Jan 10, 2020
cf66871
Add a sample number check to avoid the error
Jan 10, 2020
e3daed9
See if suppressing the warning for the bin overlap helps.
Jan 10, 2020
9a03085
Fix logic statement for sample check.
Jan 10, 2020
7cb1f8b
Remove histology groups if they don't have at least 2 samples
Jan 10, 2020
06dfed6
Merge remote-tracking branch 'upstream/master' into cin_setup
Jan 10, 2020
3625d55
Merge branch 'master' into cin_setup
cansavvy Jan 10, 2020
7f622b7
update notebook
Jan 10, 2020
fe78ff8
Merge branch 'master' into cin_setup
cansavvy Jan 10, 2020
8531d20
Fix plot zipping to overwrite current zip files
Jan 13, 2020
9a746bb
The easy changes suggested by @jashapiro have been implemented
Jan 13, 2020
e2cf01d
Heatmap is mostly there.
Jan 14, 2020
267b2f2
Merge branch 'master' into cin_setup
cansavvy Jan 14, 2020
3aa31de
Upload the heatmaps and fixed stuff
Jan 14, 2020
3f0b142
Merge remote-tracking branch 'origin/cin_setup' into cin_setup
Jan 14, 2020
e7c70bd
Merge branch 'master' into cin_setup
cansavvy Jan 14, 2020
9a61060
Incorporating @jashapiro 's suggestions
cansavvy Jan 16, 2020
6a505bd
relinter, refresh and re-run
cansavvy Jan 16, 2020
8620516
Merge branch 'master' into cin_setup
cansavvy Jan 16, 2020
4c2f7b5
Update README
cansavvy Jan 16, 2020
c608d27
Merge branch 'master' into cin_setup
jashapiro Jan 18, 2020
aec0cb9
Remove accidentally duplicated line.
jashapiro Jan 18, 2020
4e991ac
Merge branch 'master' into cin_setup
jaclyn-taroni Jan 18, 2020
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3 changes: 3 additions & 0 deletions .circleci/config.yml
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Expand Up @@ -128,6 +128,9 @@ jobs:
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"

- run:
name: Chromosomal instability breakpoints
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/chromosomal-instability/chromosomal-instability.Rmd', clean = TRUE)"

################################
#### Add your analysis here ####
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1 change: 1 addition & 0 deletions analyses/README.md
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Expand Up @@ -11,6 +11,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist

| Module | Input Files | Brief Description | Output Files Consumed by Other Analyses |
|--------|-------|-------------------|--------------|
| [`chromosomal-instability`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/chromosomal-instability) | `pbta-histologies.tsv`, `pbta-sv-manta.tsv.gz` and `pbta-cnv-cnvkit.seg.gz` | Evaluates chromosomal instability by calculating chromosomal breakpoint densities | N/A
| [`cnv-chrom-plot`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/cnv-chrom) | `pbta-cnv-cnvkit-gistic.zip` and `pbta-cnv-cnvkit.seg.gz` | Makes plots from GISTIC output as well as `seg.mean` plots by histology group | N/A
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@jashapiro jashapiro Jan 18, 2020 •
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Accidentally duplicated this line.

Suggested change
| [`cnv-chrom-plot`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/cnv-chrom) | `pbta-cnv-cnvkit-gistic.zip` and `pbta-cnv-cnvkit.seg.gz` | Makes plots from GISTIC output as well as `seg.mean` plots by histology group | N/A

| [`cnv-comparison`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/cnv-comparison) | Earlier version of SEG files | *Deprecated*; compared earlier version of the CNV methods. | N/A
| [`collapse-rnaseq`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/collapse-rnaseq) | `pbta-gene-expression-rsem-fpkm.polya.rds`, `pbta-gene-expression-rsem-fpkm.stranded.rds`, `gencode.v27.primary_assembly.annotation.gtf.gz` | Collapses RSEM FPKM matrices such that gene symbols are de-duplicated. | `results/pbta-gene-expression-rsem-fpkm-collapsed.polya.rds`, `results/pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` (included in data download; too large for tracking via GitHub)
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2 changes: 1 addition & 1 deletion analyses/chromosomal-instability/README.md
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Expand Up @@ -42,4 +42,4 @@ The individual sample plots and grouped by `short_histology` plots are in the `p
- `make_granges` : Given a data.frame with chr break coordinates, make a `GenomicRanges` object.
- `break_density`: Given data.frame(s) with chr break coordinates, calculate the density of the breaks.
- `map_density_plot`: Given a `GenomicRanges` object, use map the chromosomal coordinates to a `ggplot2`
- `chr_break_plot`: Given a list of `GenomicRanges` objects, plot them in a combined `cowplot`.
- `multipanel_break_plot`: Given a list of `GenomicRanges` objects, plot them in a combined `cowplot`.
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