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

* It's a start of a notebook

* Got some of the code converted and working

* Percent genome change plot added

* Have overlap of CNV and SV

* Breakpoint summary df

* Got things mostly organized and the wrangling functions are formed up more

* Load my functions as they are so far. TileGenome setting up

* Made a plotting function that probably won't work yet

* Things are here, just need to test things, reorg and add more doc

* Plotting function works

* It's working!

* Plots are working just need more doc

* Add a README and change the function file name

* Some reorganization and adding the plots

* lintered and neatened up some things

* Few more touches to the README

* Add the functions

* Edited a messed up comment

* Fixed some issues with the functions

* Add tumor type plots

* Rearrange and fix some things with the group calculations

* Smoothing out some metadata handling of GenomicRanges

* Functions handle multiple samples

* The functions handle grouped data

* Got rid of a development remnant I found

* minor typo fixes

* Apply percentage filter to CNV data

* Minor edits

* Changes to logic and plot names

* Incorporate @sjspielman suggestions

* Missed a paranthesis

* re-linter

* Reorganize the plots

* Add tumor type plots

* Add to CircleCI

* Get rid of development remnant

* Delete sample PNGs and zip up tumor type PNGs

* some svcnvplus files snuck in.

* Fix tumor-type plots and add automatic zip

* Get rid of 01-process-sv-file.R source step. Use straight file.

* Had to change sample name getter step

* Fix a missing `dplyr::`

* Add chromosomal instability to main README table

* Add a sample number check to avoid the error

* See if suppressing the warning for the bin overlap helps.

* Fix logic statement for sample check.

* Remove histology groups if they don't have at least 2 samples

* update notebook

* Fix plot zipping to overwrite current zip files

* The easy changes suggested by @jashapiro have been implemented

* Heatmap is mostly there.

* Upload the heatmaps and fixed stuff

* Incorporating @jashapiro 's suggestions

* relinter, refresh and re-run

* Update README

* Remove accidentally duplicated line.

Co-authored-by: jashapiro <jashapiro@gmail.com>
Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>

.circleci/config.yml

@@ -128,6 +128,10 @@ 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)"
+
       - run:
           name: Fusion Summary
           command: ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh"

analyses/README.md

@@ -11,7 +11,8 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
 
 | Module | Input Files | Brief Description | Output Files Consumed by Other Analyses |
 |--------|-------|-------------------|--------------|
-| [`cnv-chrom-plot`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/cnv-chrom) | `pbta-cnv-cnvkit-gistic.zip` <br> `pbta-cnv-cnvkit.seg.gz` | Makes plots from GISTIC output as well as `seg.mean` plots by histology group  | N/A
+| [`chromosomal-instability`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/chromosomal-instability) | `pbta-histologies.tsv` <br> `pbta-sv-manta.tsv.gz` <br> `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` <br> `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` <br> `pbta-gene-expression-rsem-fpkm.stranded.rds` <br> `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` <br> `results/pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` (included in data download; too large for tracking via GitHub)
 | [`comparative-RNASeq-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/comparative-RNASeq-analysis) | `pbta-gene-expression-rsem-tpm.polya.rds` <br> `pbta-gene-expression-rsem-tpm.stranded.rds` | *In progress*; will produce expression outlier profiles per [#229](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/229) | N/A |

analyses/chromosomal-instability/README.md

@@ -41,5 +41,5 @@ 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`.
+- `map_breaks_plot`: Given a `GenomicRanges` object, use map the chromosomal coordinates to a `ggplot2`
+- `multipanel_break_plot`: Given a list of `GenomicRanges` objects, plot them in a combined `cowplot`.