Mann whitney test #518

JanniRoebbecke · 2024-06-25T19:05:02Z

Description

Adds new method Mann-Whitney Test for differential Expression testing
the new Method exists in two variants one with the operation differential_expression and one the method Peptide analysis
the first takes any protein dataframe and returns a dictionary in the same format as the other methods in differential differential_expression. The output may be used to generate a volcano plot
the second takes a 'ptm_df' from the a 'PTMs per Sample' Step and returns it's output in wide format

Changes

the methods were implemented
the Forms and Step Classes have been defined
tests were implemented

Testing

tests have been implemented
import protein, meta and evidence file
preprocess
add Mann-Whitney Test with operation differential_expression and calculate
add 'PTMs per Sample' Step and Mann-Whitney Test with operation Peptide analysis after that and calculate

PR checklist

Development

If necessary, I have updated the documentation (README, docstrings, etc.)
If necessary, I have created / updated tests.

Mergeability

main-branch has been merged into local branch to resolve conflicts
The tests and linter have passed AFTER local merge
The code has been formatted with black

Code review

I have self-reviewed my code.
At least one other developer reviewed and approved the changes

* untested working, needs cleanup * linter * remove dupliacte method (merge screw-up) * add doc strings, fix first few tests (miss. args) * metadata df now optional param + adjusted asserts, fixed test * formatting * conditional metadata input for protein graphs * import logging levels, formatting * add grouping tests for peptides, add error handling * spelling, formatting * remove unused import, format * fix error msgs in tests * fix line length * Convert has_metadata to property * Use logger instead of print statement * An attempt at consistent text-casing * formatting --------- Co-authored-by: henninggaertner <[email protected]>

…thod

…apt-filtering-for-peptides

…thod

…ntested)

…-file' into peptides # Conflicts: # protzilla/importing/peptide_import.py # tests/protzilla/data_preprocessing/test_peptide_preprocessing.py # tests/protzilla/importing/test_peptide_import.py

…ics-amount # Conflicts: # protzilla/data_analysis/filter_peptieds_of_protein.py # ui/runs/forms/data_analysis.py

…ics-amount # Conflicts: # protzilla/data_analysis/ptm_analysis.py

…d_sample

# Conflicts: # tests/protzilla/data_preprocessing/test_peptide_preprocessing.py

# Conflicts: # protzilla/data_analysis/ptm_analysis.py # protzilla/methods/data_analysis.py # ui/runs/form_mapping.py # ui/runs/forms/data_analysis.py

# Conflicts: # protzilla/utilities/transform_dfs.py # ui/runs/forms/data_analysis.py

# Conflicts: # protzilla/data_analysis/differential_expression_mann_whitney.py # protzilla/methods/data_analysis.py # protzilla/utilities/transform_dfs.py # ui/runs/forms/data_analysis.py

github-actions · 2024-06-25T19:08:15Z

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
protzilla
run.py
run_helper.py
runner.py
protzilla/data_analysis
differential_expression_anova.py
differential_expression_linear_model.py
differential_expression_mann_whitney.py					263
differential_expression_t_test.py
protein_graphs.py
ptm_analysis.py					115-116, 134-136
protzilla/data_integration
di_plots.py
enrichment_analysis_gsea.py
protzilla/data_preprocessing
filter_proteins.py
outlier_detection.py
peptide_filter.py
transformation.py
protzilla/importing
ms_data_import.py					122, 276
protzilla/methods
data_analysis.py
data_preprocessing.py
importing.py					142
protzilla/utilities
transform_dfs.py
utilities.py
ui/main
settings.py
ui/runs
fields.py
views.py
views_helper.py
Project Total

The report is truncated to 25 files out of 73. To see the full report, please visit the workflow summary page.

_{This report was generated by python-coverage-comment-action}

lucatreide

lgtm

lucatreide · 2024-07-11T14:00:51Z

protzilla/data_analysis/differential_expression_mann_whitney.py

+    """
+    Perform Mann-Whitney U test on all proteins in the given intensity data frame.
+
+    @param intensity_df: A protein dataframe in typical PROTzilla long format.


In docstring parameters should be preceeded by : and not @

janni.roebbecke and others added 30 commits March 23, 2024 15:29

evidence import

fa28ee3

tests

2f0c566

filter proteins

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filter sampels

2bdae08

tests for filter_proteins with peptide file

9b983dd

tests for filter_proteins with peptide file, better mock dataframe

ba0d58e

output types

f07ff7e

added testing that only filtered Proteins are removed from peptides_df

12c1d5c

tests for filter_samples with peptide file

66cd83b

extract test that peptide filtering matches protein filtering into Me…

f18c8c4

…thod

Merge branch '456-addapt-outlier-detection-for-peptides' into 454-add…

16f71ea

…apt-filtering-for-peptides

refactor: shortened tests by integrating extracted method and mock data

2aedccd

exclude peptides

a297922

tests

7d115ff

minor fixes in test

4e738e6

minor fixes in test

d77da64

fix test that peptide filtering matches protein filtering Method

6f7d8f7

fix test that peptide filtering matches protein filtering Method

6f12a76

fix test that peptide filtering matches protein filtering Method

f635008

fix test that peptide filtering matches protein filtering Method

cd8fa06

match mock protein dataframe to mock peptide dataframe

f62b4f6

extract test that peptide filtering matches protein filtering into Me…

1c73f76

…thod

implementation

83fd7a5

tests

1766d36

tests improve error logging

6584acd

tests git testing

f578555

peptide import added missing column

3bf6a7d

implements form, form_mapping, method and the actual functionality (u…

92de960

…ntested)

Merge remote-tracking branch 'refs/remotes/origin/452-import-evidence…

25f15e8

…-file' into peptides # Conflicts: # protzilla/importing/peptide_import.py # tests/protzilla/data_preprocessing/test_peptide_preprocessing.py # tests/protzilla/importing/test_peptide_import.py

janni.roebbecke added 21 commits June 11, 2024 16:42

Merge branch 'refs/heads/dev' into filter-peptides-step

7cf4f70

Merge branch 'refs/heads/filter-peptides-step' into ptm-basic-statist…

82b7940

…ics-amount # Conflicts: # protzilla/data_analysis/filter_peptieds_of_protein.py # ui/runs/forms/data_analysis.py

complete merge

639561e

rename file and fix selecting multiple proteins

0f5c4b8

Merge branch 'refs/heads/filter-peptides-step' into ptm-basic-statist…

8b708d3

…ics-amount # Conflicts: # protzilla/data_analysis/ptm_analysis.py

improve efficiency of methods ptms_per_sample and ptms_per_protein_an…

e96e9cb

…d_sample

added test for ptms_per_protein_and_sample

962d680

Merge branch 'refs/heads/dev' into ptm-basic-statistics-amount

037e250

# Conflicts: # tests/protzilla/data_preprocessing/test_peptide_preprocessing.py

complete merge (fix testes after merge)

abb974b

cleanup

be45b72

Merge branch 'refs/heads/dev' into ptm-basic-statistics-amount

65bf3b0

# Conflicts: # protzilla/data_analysis/ptm_analysis.py # protzilla/methods/data_analysis.py # ui/runs/form_mapping.py # ui/runs/forms/data_analysis.py

implement differential expression with mann-whitney-test on ptm data

647e5cd

implement differential expression with mann-whitney-test on protein data

d310234

refactor input and output handling for Mann-Whitney-test on ptm data

8359f90

Merge branch 'refs/heads/dev' into mann-whitney-test

a5d4a0b

# Conflicts: # protzilla/utilities/transform_dfs.py # ui/runs/forms/data_analysis.py

Merge branch 'refs/heads/dev' into mann-whitney-test

7cd0d58

# Conflicts: # protzilla/data_analysis/differential_expression_mann_whitney.py # protzilla/methods/data_analysis.py # protzilla/utilities/transform_dfs.py # ui/runs/forms/data_analysis.py

add additional parameter form user and docstrings

c984f37

fix typo

93441fe

add test for mann whitney on intensity data

9d056a4

add test for mann whitney on ptm data

d5194c0

add mann whitney to volcano plot form

a566c24

JanniRoebbecke requested a review from lucatreide June 25, 2024 19:05

JanniRoebbecke self-assigned this Jun 25, 2024

add missing value to output_keys of mann whitney test

f459214

lucatreide approved these changes Jul 11, 2024

View reviewed changes

janni.roebbecke and others added 2 commits August 14, 2024 20:52

Implement requested changes

bd8d77d

Merge branch 'dev' into mann-whitney-test

efc072a

JanniRoebbecke merged commit e6c29e2 into dev Aug 14, 2024
1 check passed

JanniRoebbecke deleted the mann-whitney-test branch August 14, 2024 18:57

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Mann whitney test #518

Mann whitney test #518

JanniRoebbecke commented Jun 25, 2024

github-actions bot commented Jun 25, 2024 •

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lucatreide left a comment

lucatreide Jul 11, 2024

Mann whitney test #518

Mann whitney test #518

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JanniRoebbecke commented Jun 25, 2024

Description

Changes

Testing

PR checklist

github-actions bot commented Jun 25, 2024 • edited Loading

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github-actions bot commented Jun 25, 2024 •

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