Enable volcano plot with ptm data

[JanniRoebbecke]

Description

• enables the volcano plot method to be executed with differential expression data on PTMs

Changes

• The Internal function create_volcano_plot was made more versatile by removing all references to specific column names (Protein ID), thus enabling the function to take any data frame as input.
• Additionally all variable names referencing proteins have been changed to more broad names.
• The Step class automatically identifys whether the input comes from a Step on Protien or PTM data and handes that over as a parameter.
• The Method form was changed to identify all steps with the necessary output keys corrected_p_values_df and log2_fold_change_df and provide them to the user to choose which one to take the output from.
• inorder to do this the get_instance_identifyer function was changed. It can now take either one or a list of output keys and only returns identifyers of Steps, that have all the given keys in their output.

Testing

• execute the volcano plot on both differential expression tests on PTM data as well as Protein Data

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]

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
steps.py					358-359
protzilla/data_analysis
differential_expression_helper.py					125, 143
differential_expression_kruskal_wallis.py					227
differential_expression_linear_model.py
differential_expression_mann_whitney.py					266
differential_expression_t_test.py
protein_graphs.py
ptm_analysis.py					74, 119-120, 138-140
protzilla/data_integration
di_plots.py
protzilla/data_preprocessing
outlier_detection.py
transformation.py
protzilla/importing
ms_data_import.py					122, 276
protzilla/methods
data_analysis.py					21, 174, 250, 275-277, 281-283, 304-308, 351, 387-389, 916, 935
data_preprocessing.py
importing.py					144
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					318-322, 379, 409, 445, 468, 504-508, 513, 1183, 1224-1228, 1252
Project Total

The report is truncated to 25 files out of 55. To see the full report, please visit the workflow summary page.

This report was generated by python-coverage-comment-action