Draft initial CNV evidence view plot data wrangling and plotting scripts

[kelseykeith]

Draft plots for CNV visualizations to be added to the API were made, but the code needs to be transformed from the development code to final scripts that can make a plot for any cancer and gene, rather than the specific genes selected for demoing, as mentioned in PediatricOpenTargets/ticket-track #288. Starting with the simplest plot proposed, the simpler plot for the evidence page view to reduce complexity while learning how to integrated plots into the API. Example of the proposed plot:

The following two scripts need to be created, based off of the modified demo code:

• One script that formats consensus_wgs_plus_cnvkit_wxs.tsv, plus any necessary additional metadata files like histologies.tsv, into a single CSV that can be used to make a plot for all combinations of cancer_group/EFO_ID and Ensembl ID ensg_id.
• One script that creates the simple stacked bar plot evidence plot based on given EFO ID and ensembl ID.

These scripts will most likely need to be modified as development to add this plot into the API continues.

Also will need to create a CNV API Design doc to share with stakeholders based on the document created for the TPM plots.

[kelseykeith]

Data wrangling code will need to be updated once https://github.com/PediatricOpenTargets/ticket-tracker/issues/437 is completed and takes care of the duplicated CNV calls. This will also dictate which commit of OpenPedCan-analysis the CNV code will need to be developed under

[kelseykeith]

Closing this ticket with the addition of draft code added in https://github.com/PediatricOpenTargets/OpenPedCan-api/commit/6aa2ddad65432f187e8b498c101c1251d648f951. There is also an example file attached that can be run with the data from OpenPedCan-analysis to produce an example plot for the gene GPC2 in Neuroblastoma. (The code file is attached as a markdown file because GitHub doesn't support upload of Rmd in comments. A knitted pdf version is also attached for looking at the results.)

evidence_plot_draft_code.md evidence_plot_draft_code.pdf