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

.circleci/config.yml

@@ -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 ####

analyses/README.md

@@ -11,6 +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 |
 |--------|-------|-------------------|--------------|
+| [`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
 | [`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)

analyses/chromosomal-instability/README.md

@@ -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`.