msreport 0.0.33__tar.gz → 0.0.34__tar.gz

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Files changed (96) hide show
  1. {msreport-0.0.33 → msreport-0.0.34}/CHANGELOG.md +10 -0
  2. {msreport-0.0.33 → msreport-0.0.34}/PKG-INFO +1 -1
  3. {msreport-0.0.33 → msreport-0.0.34}/msreport/__init__.py +1 -1
  4. {msreport-0.0.33 → msreport-0.0.34}/msreport/analyze.py +2 -2
  5. {msreport-0.0.33 → msreport-0.0.34}/.gitignore +0 -0
  6. {msreport-0.0.33 → msreport-0.0.34}/LICENSE.txt +0 -0
  7. {msreport-0.0.33 → msreport-0.0.34}/README.md +0 -0
  8. {msreport-0.0.33 → msreport-0.0.34}/msreport/aggregate/__init__.py +0 -0
  9. {msreport-0.0.33 → msreport-0.0.34}/msreport/aggregate/condense.py +0 -0
  10. {msreport-0.0.33 → msreport-0.0.34}/msreport/aggregate/pivot.py +0 -0
  11. {msreport-0.0.33 → msreport-0.0.34}/msreport/aggregate/summarize.py +0 -0
  12. {msreport-0.0.33 → msreport-0.0.34}/msreport/errors.py +0 -0
  13. {msreport-0.0.33 → msreport-0.0.34}/msreport/export.py +0 -0
  14. {msreport-0.0.33 → msreport-0.0.34}/msreport/fasta.py +0 -0
  15. {msreport-0.0.33 → msreport-0.0.34}/msreport/helper/__init__.py +0 -0
  16. {msreport-0.0.33 → msreport-0.0.34}/msreport/helper/calc.py +0 -0
  17. {msreport-0.0.33 → msreport-0.0.34}/msreport/helper/maxlfq.py +0 -0
  18. {msreport-0.0.33 → msreport-0.0.34}/msreport/helper/table.py +0 -0
  19. {msreport-0.0.33 → msreport-0.0.34}/msreport/helper/temp.py +0 -0
  20. {msreport-0.0.33 → msreport-0.0.34}/msreport/impute.py +0 -0
  21. {msreport-0.0.33 → msreport-0.0.34}/msreport/isobar.py +0 -0
  22. {msreport-0.0.33 → msreport-0.0.34}/msreport/normalize.py +0 -0
  23. {msreport-0.0.33 → msreport-0.0.34}/msreport/peptidoform.py +0 -0
  24. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/__init__.py +0 -0
  25. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/_partial_plots.py +0 -0
  26. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/comparison.py +0 -0
  27. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/distribution.py +0 -0
  28. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/multivariate.py +0 -0
  29. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/quality.py +0 -0
  30. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/style.py +0 -0
  31. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/style_sheets/_all_relevant_styles.md +0 -0
  32. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/style_sheets/msreport-notebook.mplstyle +0 -0
  33. {msreport-0.0.33 → msreport-0.0.34}/msreport/plot/style_sheets/seaborn-whitegrid.mplstyle +0 -0
  34. {msreport-0.0.33 → msreport-0.0.34}/msreport/qtable.py +0 -0
  35. {msreport-0.0.33 → msreport-0.0.34}/msreport/reader.py +0 -0
  36. {msreport-0.0.33 → msreport-0.0.34}/msreport/rinterface/__init__.py +0 -0
  37. {msreport-0.0.33 → msreport-0.0.34}/msreport/rinterface/limma.py +0 -0
  38. {msreport-0.0.33 → msreport-0.0.34}/msreport/rinterface/rinstaller.py +0 -0
  39. {msreport-0.0.33 → msreport-0.0.34}/msreport/rinterface/rscripts/limma.R +0 -0
  40. {msreport-0.0.33 → msreport-0.0.34}/pyproject.toml +0 -0
  41. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/.gitignore +0 -0
  42. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/common/table.txt +0 -0
  43. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/SampleA_1/ion.tsv +0 -0
  44. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/SampleA_1/peptide.tsv +0 -0
  45. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/SampleA_1/protein.tsv +0 -0
  46. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/SampleA_1/psm.tsv +0 -0
  47. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/SampleB_1/ion.tsv +0 -0
  48. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/SampleB_1/peptide.tsv +0 -0
  49. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/SampleB_1/protein.tsv +0 -0
  50. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/SampleB_1/psm.tsv +0 -0
  51. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/combined_ion.tsv +0 -0
  52. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/combined_modified_peptide.tsv +0 -0
  53. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/combined_peptide.tsv +0 -0
  54. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/fragpipe/combined_protein.tsv +0 -0
  55. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/maxquant/evidence.txt +0 -0
  56. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/maxquant/peptides.txt +0 -0
  57. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/maxquant/proteinGroups.txt +0 -0
  58. {msreport-0.0.33 → msreport-0.0.34}/tests/_OLD_testdata/spectronaut/table_spectronaut_style_tag.txt +0 -0
  59. {msreport-0.0.33 → msreport-0.0.34}/tests/test_aggregate/test_condense.py +0 -0
  60. {msreport-0.0.33 → msreport-0.0.34}/tests/test_aggregate/test_pivot.py +0 -0
  61. {msreport-0.0.33 → msreport-0.0.34}/tests/test_aggregate/test_summarize.py +0 -0
  62. {msreport-0.0.33 → msreport-0.0.34}/tests/test_analyze.py +0 -0
  63. {msreport-0.0.33 → msreport-0.0.34}/tests/test_export.py +0 -0
  64. {msreport-0.0.33 → msreport-0.0.34}/tests/test_helper.py +0 -0
  65. {msreport-0.0.33 → msreport-0.0.34}/tests/test_impute.py +0 -0
  66. {msreport-0.0.33 → msreport-0.0.34}/tests/test_isobar.py +0 -0
  67. {msreport-0.0.33 → msreport-0.0.34}/tests/test_maxlfq.py +0 -0
  68. {msreport-0.0.33 → msreport-0.0.34}/tests/test_normalize/test_categorical_normalizer.py +0 -0
  69. {msreport-0.0.33 → msreport-0.0.34}/tests/test_normalize/test_normalize.py +0 -0
  70. {msreport-0.0.33 → msreport-0.0.34}/tests/test_peptidoform.py +0 -0
  71. {msreport-0.0.33 → msreport-0.0.34}/tests/test_plot.py +0 -0
  72. {msreport-0.0.33 → msreport-0.0.34}/tests/test_qtable.py +0 -0
  73. {msreport-0.0.33 → msreport-0.0.34}/tests/test_reader/test_fragpipe.py +0 -0
  74. {msreport-0.0.33 → msreport-0.0.34}/tests/test_reader/test_maxquant.py +0 -0
  75. {msreport-0.0.33 → msreport-0.0.34}/tests/test_reader/test_reader_functions.py +0 -0
  76. {msreport-0.0.33 → msreport-0.0.34}/tests/test_reader/test_resultreader.py +0 -0
  77. {msreport-0.0.33 → msreport-0.0.34}/tests/test_reader/test_spectronaut.py +0 -0
  78. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/common/table.txt +0 -0
  79. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/SampleA_1/ion.tsv +0 -0
  80. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/SampleA_1/peptide.tsv +0 -0
  81. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/SampleA_1/protein.tsv +0 -0
  82. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/SampleA_1/psm.tsv +0 -0
  83. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/SampleB_1/ion.tsv +0 -0
  84. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/SampleB_1/peptide.tsv +0 -0
  85. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/SampleB_1/protein.tsv +0 -0
  86. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/SampleB_1/psm.tsv +0 -0
  87. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/combined_ion.tsv +0 -0
  88. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/combined_modified_peptide.tsv +0 -0
  89. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/combined_peptide.tsv +0 -0
  90. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/combined_protein.tsv +0 -0
  91. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/fragpipe/fragpipe-files.fp-manifest +0 -0
  92. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/maxquant/evidence.txt +0 -0
  93. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/maxquant/peptides.txt +0 -0
  94. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/maxquant/proteinGroups.txt +0 -0
  95. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/spectronaut/ConditionSetup.tsv +0 -0
  96. {msreport-0.0.33 → msreport-0.0.34}/tests/testdata/spectronaut/table_spectronaut_style_tag.txt +0 -0
{msreport-0.0.33 → msreport-0.0.34}/CHANGELOG.md RENAMED
@@ -1,5 +1,15 @@
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  # Changelog
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+ ----------------------------------------------------------------------------------------
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+
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+ ## 0.0.34 - Hotfix: Multi-group LIMMA
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+ Released: 2026-02-05
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+
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+ ### Fixed
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+ - Fix `analysis.calculate_multi_group_limma` output columns to correctly include comparison pairs (e.g., "P-value exp1 vs exp2") instead of generic metric names.
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+
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+ ----------------------------------------------------------------------------------------
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+
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  ## 0.0.33 - Enhanced Statistics
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  Released: 2026-02-05
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{msreport-0.0.33 → msreport-0.0.34}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: msreport
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- Version: 0.0.33
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+ Version: 0.0.34
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  Summary: Post processing and analysis of quantitative proteomics data
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  Project-URL: homepage, https://github.com/hollenstein/msreport
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  Project-URL: documentation, https://hollenstein.github.io/msreport/
{msreport-0.0.33 → msreport-0.0.34}/msreport/__init__.py RENAMED
@@ -3,7 +3,7 @@ from msreport.fasta import import_protein_database
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  from msreport.qtable import Qtable
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  from msreport.reader import FragPipeReader, MaxQuantReader, SpectronautReader
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- __version__ = "0.0.33"
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+ __version__ = "0.0.34"
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  __all__ = [
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  "analyze",
{msreport-0.0.33 → msreport-0.0.34}/msreport/analyze.py RENAMED
@@ -672,7 +672,7 @@ def calculate_multi_group_limma(
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  experiment_pair = [r_to_experiment[s] for s in r_comparison_group.split("-")]
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  comparison_group = comparison_tag.join(experiment_pair)
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  mapping = {col: f"{col} {comparison_group}" for col in limma_result.columns}
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- limma_result = limma_result.rename(columns=mapping)
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+ limma_results[r_comparison_group] = limma_result.rename(columns=mapping)
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  limma_table = pd.DataFrame(index=table.index)
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  limma_table = limma_table.join(list(limma_results.values()))
@@ -790,7 +790,7 @@ def calculate_two_group_limma(
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  if batch:
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  design_df = qtable.get_design().set_index("Sample")
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  batch_groups = [str(design_df.loc[s, "Batch"]) for s in table.columns]
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- print(table[mask])
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+
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  # Note that the order of experiments for calling limma is reversed
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  limma_result = msreport.rinterface.two_group_limma(
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  table[mask],
{msreport-0.0.33 → msreport-0.0.34}/.gitignore RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/LICENSE.txt RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/README.md RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/msreport/errors.py RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/msreport/export.py RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/msreport/fasta.py RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/msreport/impute.py RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/msreport/isobar.py RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/msreport/qtable.py RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/msreport/reader.py RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/pyproject.toml RENAMED
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{msreport-0.0.33 → msreport-0.0.34}/tests/test_plot.py RENAMED
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