Add several plotting scripts by FerriolCalvet · Pull Request #333 · bbglab/deepCSA

FerriolCalvet · 2025-07-29T15:25:32Z

Still missing some plots but this is a partial plotting update to get several plots to dev so that it can start to be used.

AI generated summary

This pull request introduces significant updates to the plotting workflows and configuration of the deepcsa pipeline, focusing on modularization, improved plotting capabilities, and better handling of omega analysis outputs. Key changes include the addition of new processes and workflows for plotting, updates to the omega analysis workflow, and the replacement of individual plot modules with a centralized plotting summary workflow.

Plotting Enhancements:

Added a new process PLOT_SATURATION in modules/local/plot/saturation/main.nf for generating saturation plots, including inputs, outputs, and the necessary script logic.
Introduced a new workflow PLOTTING_SUMMARY in subworkflows/local/plottingsummary/main.nf to centralize and streamline the generation of selection and saturation plots. This replaces individual plot calls in the main workflow.
Updated the PLOT_SELECTION_METRICS process in modules/local/plot/selection_metrics/main.nf to simplify arguments and output handling, and ensure output directories are created consistently. [1] [2]

Omega Analysis Workflow Updates:

Enhanced the OMEGA_ANALYSIS workflow in subworkflows/local/omega/main.nf by adding empty channels for site_comparison_results and global_loc_results to handle outputs more flexibly.
Modified the workflow to flatten and emit site_comparison_results for downstream use, ensuring compatibility with the new plotting summary workflow. [1] [2]

Integration into Main Workflow:

Replaced the PLOT_SELECTION_METRICS module with the new PLOTTING_SUMMARY workflow in workflows/deepcsa.nf, integrating it with the omega analysis and positive selection results. [1] [2]
Updated the workflow logic to ensure PLOTTINGSUMMARY is invoked only when all required parameters (omega, oncodrive3d, oncodrivefml, indels) are enabled.

Configuration Adjustments:

Added a new parameter omega_plot to the conf/test_real.config file to toggle omega plot generation.

These changes improve the modularity, maintainability, and functionality of the pipeline, particularly in the context of plotting and omega analysis.

- subworkflow definition - shortlisting plots to add missing: - nf scripts for the modules - python scripts for the plots

list inputs

missing: - handle sample information input files - handle reference datasets - handle multiple genes

- not tested - pending to decide creation of unique_splice_sites

commit 10c12aa Author: FerriolCalvet <ferriolcalvet@gmail.com> Date: Thu Jul 24 12:35:40 2025 +0200 update gnomAD threshold to 0.001 - ignore errors in omega plot commit 31e741e Author: FerriolCalvet <ferriolcalvet@gmail.com> Date: Tue Jul 22 18:34:11 2025 +0200 update description and fix broken link commit 7b0fd9b Merge: 72dc4d9 cb18adc Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Sun Jul 20 22:34:46 2025 +0200 Merge pull request #315 from bbglab/dev commit cb18adc Author: FerriolCalvet <ferriolcalvet@gmail.com> Date: Sat Jul 19 12:40:39 2025 +0200 fix bug in mut density & update omega container commit 1b4a52d Author: FerriolCalvet <ferriolcalvet@gmail.com> Date: Tue Jul 15 15:52:07 2025 +0200 fix broken path for test_real commit db6d640 Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Fri Jul 11 15:50:45 2025 +0200 Allow gene selection in consensus (#316) * update consensus building to filter genes - add consensus compliance param - add list of genes param - NOT tested * tested gene filter implementation - consensus panels implemented in polars - allowing subset for specific genes commit b92c2b9 Author: FerriolCalvet <ferriolcalvet@gmail.com> Date: Thu Jul 10 23:56:47 2025 +0200 add metro map commit 11fb1c5 Author: FerriolCalvet <ferriolcalvet@gmail.com> Date: Thu Jul 10 08:25:31 2025 +0200 update description in main README commit 628f282 Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Mon Jul 7 19:14:21 2025 +0200 Add more complete docs (#306) * first doc update * update in usage documentation - list params - list structural parameters and files * backbone of output docs * update usage description with custom sets of mutations * fix headers * docs: Update usage with vep information * update output description * update order of usage information * update distribution of information in the docs * fix typo in docs/output.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix markdown linting * remove unnecessary validation params from config - REQUIRES TESTING * remove remaining references to download VEP cache * update dag format to mmd * update in usage * update documentation of file formatting and some params * add examples in file formatting docs * apply review comments * remove Nextflow parameters section * minor fix in nextflow.config --------- Co-authored-by: Miquel L. Grau <miguel.grau@irbbarcelona.org> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> commit 72dc4d9 Author: FerriolCalvet <ferriolcalvet@gmail.com> Date: Mon Jul 7 15:53:47 2025 +0200 temporary LICENSE definition commit 14c5246 Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Fri Jun 27 11:19:45 2025 +0200 fix bug in panel_annotation (#313) reimplement it with click solved the problem - only_canonical boolean working - not tested commit 764782a Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Thu Jun 26 23:23:05 2025 +0200 Update mutation rate to mutation density (#307) * rename mutrate to mut density - reimplement with click - partial renaming - simplification of sample_name logic * full update of mutation rate to mutation density * define other_sample_SNP based on all VAF * update mutation density functions - clean code - add explanation on mutation density * apply review changes commit aae8f0b Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Thu Jun 26 10:49:00 2025 +0200 Ensure POSTPROCESSVEPPANEL in output (#311) * fix relative mutabilities output * explicitly define postprocessveppanel outdir * force outputting postprocesspanel * update storing fixes commit dd25b9b Merge: 05c80ee 26d5d9b Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Wed Jun 4 23:09:29 2025 +0200 Merge pull request #303 from bbglab/dev First pre-release merge commit 05c80ee Merge: ea9a301 e06218a Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Tue Apr 29 10:30:23 2025 +0200 Merge pull request #289 from bbglab/tmp-dev First release commit e06218a Merge: 7559d7f ea9a301 Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Date: Tue Apr 29 10:11:05 2025 +0200 Merge branch 'main' into tmp-dev commit ea9a301 Author: FerriolCalvet <ferriolcalvet@gmail.com> Date: Thu Jul 25 16:05:10 2024 +0200 update schema

- NOT WORKING

- add mutation types

- collect sitecomparisons - remove reference to ddg. requires external - fix input unique to keep header and minimal information - tested and works

FerriolCalvet

I think all looks good for now

FedericaBrando

I've checked the files and gave a broad overview of the code. I think overall is a good improvement in terms of logic and organization. Most of my comments refers to the dead code present in the code base that should either removed or explained.

A minor issue may arise if the request is looped forever and r.ok is never True. I would add a limit, an exception or a raise (whatever fits best).

Good job! 💯

bin/plot_gene_saturation.py

bin/plot_selectionsideplots.py

modules/local/plot/saturation/main.nf

- temporary solution to domain information loading

- subset domains to in_panel ones - update domain name definition - plotting modules works - missing autoexons plot - update signatures output

- add general error handling to all plotting modules - generate exons bedfile within panel

- use correct exons definition - update custom bedfile name - not tested

Copilot

Pull Request Overview

This PR introduces significant plotting and analysis workflow improvements to the deepcsa pipeline, focusing on centralized plotting capabilities and enhanced omega analysis integration. The changes modularize plotting functionality while improving the handling of selection analysis outputs.

Replaces individual plot modules with a centralized PLOTTING_SUMMARY workflow
Enhances omega analysis workflow to better handle site comparison and plotting outputs
Updates parameter naming from omega_hotspots_bedfile to omega_subgenic_bedfile for clarity

Reviewed Changes

Copilot reviewed 22 out of 34 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Integrates new plotting summary workflow and updates DNA2PROTEIN mapping inputs
subworkflows/local/plottingsummary/main.nf	New centralized plotting workflow combining selection and saturation plots
subworkflows/local/omega/main.nf	Enhanced to emit site comparison results and support new plotting workflow
modules/local/plot/saturation/main.nf	New process for generating saturation plots with comprehensive inputs
modules/local/plot/selection_metrics/main.nf	Simplified argument handling and standardized output directory creation
Various config files	Parameter renaming from `omega_hotspots_bedfile` to `omega_subgenic_bedfile`

subworkflows/local/plottingsummary/main.nf

subworkflows/local/omega/main.nf

modules/local/expand_regions/main.nf

workflows/deepcsa.nf

FerriolCalvet and others added 16 commits June 16, 2025 12:04

plotting wishlist

f5af63d

- subworkflow definition - shortlisting plots to add missing: - nf scripts for the modules - python scripts for the plots

add raw version of supplementary figure plotting

467243a

update omega plotting

0f076a3

plotting update: omega & needles & stacked

8f50806

update plotting cohort plots working

99098cb

clean code

14577cf

list inputs

saturation data loading working

ffc9709

gene saturation all tracks working with TP53

6d92ce3

tested additional complementary plots

52aa080

missing: - handle sample information input files - handle reference datasets - handle multiple genes

update gene saturation inputs from pipeline

1b978b5

- not tested - pending to decide creation of unique_splice_sites

update stacked plot needles

48b47b2

minor fixes after merge

98fda9e

- NOT WORKING

update linewidth and size

54daa41

- add mutation types

fix plot saturation within pipeline

ff9d46d

- collect sitecomparisons - remove reference to ddg. requires external - fix input unique to keep header and minimal information - tested and works

Merge branch 'dev' into massive-plotting

43430ed

FerriolCalvet commented Jul 29, 2025

View reviewed changes

FerriolCalvet requested a review from Copilot July 29, 2025 15:33

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fix o3d logs output

c5e0d29

FerriolCalvet requested a review from FedericaBrando July 29, 2025 16:03

plot multiple genes, not only TP53

7c96976

FedericaBrando reviewed Jul 29, 2025

View reviewed changes

FerriolCalvet and others added 3 commits July 30, 2025 00:00

apply review suggestions

f4841d0

- temporary solution to domain information loading

Merge branch 'dev' into massive-plotting

666892e

update domain definition and plotting

7064dd1

- subset domains to in_panel ones - update domain name definition - plotting modules works - missing autoexons plot - update signatures output

FerriolCalvet self-assigned this Jul 31, 2025

FerriolCalvet linked an issue Jul 31, 2025 that may be closed by this pull request

Needle plots by bins #159

Closed

FerriolCalvet added 2 commits July 31, 2025 17:43

- separate generation of depth per exon

2a3c3bc

- add general error handling to all plotting modules - generate exons bedfile within panel

batch update of exon definitions

4164291

- use correct exons definition - update custom bedfile name - not tested

fix exons panel generation

329baec

FerriolCalvet requested a review from Copilot August 1, 2025 08:09

Merge branch 'dev' into massive-plotting

1927370

Copilot AI reviewed Aug 1, 2025

View reviewed changes

add error handling to omega plot

831fea6

FerriolCalvet merged commit fd48355 into dev Aug 1, 2025

FerriolCalvet deleted the massive-plotting branch August 11, 2025 21:36

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Add several plotting scripts#333

Add several plotting scripts#333
FerriolCalvet merged 26 commits intodevfrom
massive-plotting

FerriolCalvet commented Jul 29, 2025 •

edited

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FerriolCalvet commented Jul 29, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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AI generated summary

Plotting Enhancements:

Omega Analysis Workflow Updates:

Integration into Main Workflow:

Configuration Adjustments:

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Pull Request Overview

Reviewed Changes

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FerriolCalvet commented Jul 29, 2025 •

edited

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