PTM basic statistics amount

[JanniRoebbecke]

Description

• implements new methods
  1. 'ptms_per_sample': generates a dataframe with a row for every sample and column for every type of ptm in the data, with the cells containing the amount of that ptm type in the respective sample
  2. 'ptms_per_protein_and_sample': generates a dataframe with a row for every sample and a column for every protein in the data, with the cells containing a string containing a list of all ptm types (with their amount) found in that Sample and Protein

Changes

• main changes are in 'ptm_analysis.py' where the two methods where added
• 'forms/data_analysis.py', 'methods/data_analysis.py' and 'form_mapping.py' where adapted to enable the user to use the new methods

Testing

• create a new run and import an evidence file with the evidence import step
• step through data_preprocessing
• add step 'PTMs per Sample' and 'PTMs per Protein and Sample' in Section 'Data Analysis'
• calculate the steps and inspect the resulting Table

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

[github-actions[bot]]

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_t_test.py
protein_graphs.py
ptm_analysis.py					44, 64, 66-67, 70-76, 90, 96, 99, 102, 112-116, 134-139
protzilla/data_integration
di_plots.py
enrichment_analysis_gsea.py
protzilla/data_preprocessing
filter_proteins.py
outlier_detection.py
transformation.py
protzilla/importing
ms_data_import.py					122, 276
peptide_import.py
protzilla/methods
data_analysis.py					635-641, 658, 664-667, 674, 678, 681-682, 689-700
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
ui/runs/forms
data_analysis.py					927-935, 967-980, 990-1002
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