plot depths per group by efigb · Pull Request #424 · bbglab/deepCSA

efigb · 2026-02-25T11:56:49Z

This branch adds a new module to process analysis of consensus exons depth for a defined group of samples and for a subset of genes (default genes in the panel) plotting all these possibilities in an output pdf that is stored in the same output directory as plotting the depths (/depths/summary)

- branch does NOT work

…d main nextflow files to integrate in the pipeline

… as in modules main.nf

…ig , corrected process

…irectory

efigb · 2026-02-25T11:58:32Z

tested that the branch works in this seqera run

efigb · 2026-02-25T13:14:50Z

Note that to plot the groups they should be parsed in seqera as this:

features_groups_list: "[ ["BLADDER_LOCATION"], ["SEX"], ["SMOKING_STATUS"] ]"

When groups are set up in other format it will use only the first group for comparisons (in this case "BLADDER_LOCATION"):

features_groups_list: "[ ["BLADDER_LOCATION"], ["BLADDER_LOCATION", "SEX"], ["BLADDER_LOCATION", "SEX", "SMOKING_STATUS"] ]"

Checked in this run

m-huertasp

Hola!! I think this is quite a nice job! As we talked about, there are a few things that might need to be changed. I have added some comments so it is easier to check the things we discussed.

Good job!

bin/depth_group_comparison.py

modules/local/analyzedepths/main.nf

workflows/deepcsa.nf

Co-authored-by: Marta Huertas <97596516+m-huertasp@users.noreply.github.com>

…s parameter, and the output of a pdf with all plots per group. Also added a condition so this module can only run when user defines a groups list

efigb · 2026-02-25T16:36:34Z

bin/depth_group_comparison.py

+
+@click.command()
+@click.option('--table-filename', required=True, type=click.Path(exists=True), help='Input features table file')
+@click.option('--depth-table', required=True, type=click.Path(exists=True), help='Input depth table file')


@FerriolCalvet I couldn't find an output file from consensus exons depth that contains the "ALL_GENES" value per sample, so that I could use it to plot the all genes value per sample. These are the other files from the output, I used average_depth_gene_sample:

average_depth_sample = DEPTHSSUMMARY.out.average_per_sample average_depth_gene = DEPTHSSUMMARY.out.average_per_gene average_depth_gene_sample = DEPTHSSUMMARY.out.average_per_gene_sample

So the script uses the average_depth_gene_sample to plot the 'all genes' value per group of samples, and this is why the 'all genes' plots per group show more spots than the by gene per group plots. The way it handles it could be error prone so I would try to fix this with an external file.

there is no such ALL_GENES scenario, the information in the average_depth_sample is like what you would expect to have for ALL_GENES.
Maybe you could:

also take this file

define a GENE column with the value ALL_GENES

then concatenate this table to the table that you already have
and this way you would have a correct ALL_GENES value that you could plot with the rest of plots

…th plots file

conf/modules.config

…ALL_GENES values per group. Added new input in config for it. Also fixed bug in processing groups and added in modules.config a subdirectory for output

efigb · 2026-02-26T22:26:22Z

bin/depth_group_comparison.py

    # Process groups
-    groups_of_interest_init = ast.literal_eval(groups) if groups else []
-    groups_of_interest = []
-    groups_of_interest =  list(dict.fromkeys(item.strip() for sublist in groups_of_interest_init for item in sublist if item != ''))


there was a bug in this code that I had to replace to handle different type of groups:

["BLADDER_LOCATION"], ["BLADDER_LOCATION", "SEX"], ["BLADDER_LOCATION", "SEX", "SMOKING_STATUS"] ]'

and

"[ ["Sample_Group"], ["cancer"], ["Age_onset"], ["Cancer_age_group"] , ["Bacterial_Signatures_identified"]]"

efigb · 2026-02-26T22:30:42Z

bin/depth_group_comparison.py

+
+    # Process depth per sample to add the 'ALL_GENES' depth value per sample
+    print('Processing per sample depth table to add the ALL_GENES depth column: ')
+    depth_per_sample['GENE'] = 'ALL_GENES'


@FerriolCalvet if user does not define the genes in the panel as custom genes, with the way we handle it now to calculate ALL_GENES depth, it will display all depths from both on target and off target genes in the panel right? I mean the default would not be the panel genes but including off targets...

efigb · 2026-02-26T22:31:35Z

conf/modules.config

        // you will have to add an extra parameters to the pipeline (nextflow.config) and then handle it here
        publishDir = [
-            path: { "${params.outdir}/plots/depths_summary" }, 
+            path: { "${params.outdir}/plots/depths_summary/plots_per_group" }, 


now added as subdirectory specific for groups

FerriolCalvet and others added 9 commits February 24, 2026 15:18

add temporary changes

ec55eff

- branch does NOT work

minor assist

6a1a5e1

added script to plot depths per group and modified modules, config an…

9bc9e7c

…d main nextflow files to integrate in the pipeline

corrected typo

7bab0a1

corrected separator variable name in modules.config so it is the same…

714fd20

… as in modules main.nf

clarified terms in script, modified variable names for module in conf…

f9677d9

…ig , corrected process

modfied main.nf according previous commit

3d4613d

removed slash in output prefix params so it does not handle it as a d…

0e72b5e

…irectory

modified script to add extra width space in plots so title is not cut

94153bd

efigb added the new-feature New functionality being added. label Feb 25, 2026

m-huertasp self-requested a review February 25, 2026 14:31

m-huertasp reviewed Feb 25, 2026

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efigb and others added 2 commits February 25, 2026 16:41

Apply suggestions from code review

735b525

Co-authored-by: Marta Huertas <97596516+m-huertasp@users.noreply.github.com>

modified script and associated files to omit output prefix variable a…

bd9c5c9

…s parameter, and the output of a pdf with all plots per group. Also added a condition so this module can only run when user defines a groups list

efigb commented Feb 25, 2026

View reviewed changes

modified path so it is stored together with the other all samples dep…

1b7af33

…th plots file

efigb commented Feb 25, 2026

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efigb self-assigned this Feb 25, 2026

modified script to parse average depth per sample and use it to plot …

1718780

…ALL_GENES values per group. Added new input in config for it. Also fixed bug in processing groups and added in modules.config a subdirectory for output

efigb commented Feb 26, 2026

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efigb requested review from FerriolCalvet and m-huertasp February 26, 2026 22:32

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efigb commented Feb 25, 2026

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