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CHANGELOG

v0.4.1 (2024-10-22)

Documentation

  • docs(*): update installation instructions (f05d1f9)

  • docs(*): fix some formatting (c5813f6)

Fix

  • fix(denovo.signature_similarity): fix rank 1 only behaviour

changed signature_similairty to return an empty series when passed only rank 1 decompositions in line with cophenetic_correlation and dispersion. needed fix for a step in Nextflow pipeline when using k=1. (16278f5)

v0.4.0 (2024-09-30)

Feature

  • feat(denovo): add post-hoc K-W tests (#13)

Added post-hoc testing using Dunn's test to the univariate_tests method. This information is not yet displayed in the default plots. (47d2eb5)

v0.3.2 (2024-09-27)

Fix

  • fix(denovo): indicate effect direction (#12)

Added columns univariate_test output indicating which factor level has the maximum mean and median. For two group tests can use this as an indication of effect direction. (e858fb5)

v0.3.1 (2024-09-10)

Fix

  • fix(denovo): sort values by rank in stability rank select

If stability critera (coph, disp, sigsim) were not in rank order in input automated suggestions of rank would be incorrect. Internally sorts by rank now so can be provided in any order. (391a2fa)

  • fix(denovo): use online kneed

Ocassionally too low a rank was being selected from bicrossvalidation curves, where a clear elbow point was visible later. Changed kneed to use online mode by default, which scan the entire curve rather than terminating at the first elbow. (beaefae)

v0.3.0 (2024-09-05)

Documentation

  • docs: add summaries

summaries for some module and overall package added. (4b48520)

Feature

  • feat(stability): add methods to show stability of signatures (#10)

  • feat(stability): allow use of signature similarity as rank selection method. (870cd84)

v0.2.0 (2024-08-30)

Documentation

  • docs(*): micromamba troubleshooting, docstring

Fix method to make conda available to nextflow when using micromamba. Update some docstring formating to prevent newlines. Add semantic versioning to dev dependencies. (6bc8093)

Feature

  • feat(denovo): plot_metadata now can include modelfit

add model fit to the standard metadata plots. this will eventually replace plot_modelfit, but for now both exists. (36e1f7d)

  • feat(data): nsclc example data and notebook added

add case study on NSCLC atlas to documentation, and included data in the data module. (010a8e5)

  • feat(denovo): stability rank suggestion

add function to suggest ranks based on peaks for stability based measures (dispersion, cophenetic correlation) (5447016)

  • feat(denovo): change plotting backend

change relative weight plot to use marsilea remove patchwork lib update plotnine to 0.13.6 (b095e84)

  • feat(data): data subpackage added

Add data subpackage, along with ALL/AML dataset and Swimmer dataset. Move synthetic data generation method to data subpackage. Add ExamleData class to hold data and metadata for provided/synthetic datasets. (ec89c6b)

  • feat(denovo): Stability rank selection methods

Add cophenetic correlation and dispersion coefficients for rank selection and associated plots. (c780607)

Fix

  • fix(denovo): remove rank 1 from stability rank suggestion. (1829a17)

  • fix(denovo): load from tar.gz properly (8fd938e)

  • fix(denovo): allow custom colours for group in relative weight plot

plot_relative_weight now accepts parameter group_colors which is a series mapping metadata value to a colour for the ribbon element of the plot. can be blank for default Marsilea colours. (3cf28ee)

  • fix(denovo): use consistent colours for bicv measures

plot_rank_selection and plot_regu_selection now uses the same colour for each property whenever displayed, doesn't always start at the same colour. (bf8f91b)

  • fix(denovo): change to star suggested rank/alpha

plot_rank_selection and plot_regu_selection use a star at the top of the plot to indicate suggested rank rather than a dashed vertical line. (6a23b2d)

  • fix(denovo): improve handling rank 1 by stability

removes decompositions of rank 1 from calculation of stability based rank selection methods, as not meaningful. (ac80647)

  • fix(data): include swimmer data

added swimmer data to repo. (9ef625b)

  • fix(*): tidy loggers

use module loggers rather than the global logging functions (d918057)

Unknown

  • Fold design (#9)

  • feat(deono): design parameter for bicv

support different designs for bicv. rank_selection and regu_selection (and all underlying classes/functions) now take a tuple parameter design, which determines how many times to split the shuffled input during bicrossvalidation. you are no longer limitted to 3x3 9-fold cva! (04ab493)

  • Merge pull request #8 from apduncan/modelfit_plotting

Modelfit plotting (3fa104a)

  • metadata accept df. need to extend to univar tests. (1cd83c1)

  • Merge pull request #7 from apduncan/cell_example

feat(data): nsclc example data and notebook added (e070d61)

  • Merge pull request #6 from apduncan/suggest_peaks

feat(denovo): stability rank suggestion (62552fa)

  • Merge pull request #5 from apduncan/replace_patchworklib

feat(denovo): change plotting backend (cd4c2ed)

  • remove patchworklib dependencies and import (461e17f)

  • merge logging changes to marsilea work (9f52d34)

  • Initial work on replacing patchworklib (fb58280)

  • Merge pull request #4 from apduncan/logging

fix(*): tidy loggers (372d4b3)

  • Tests for data (24aa1bc)

  • Initial work on replacing patchworklib (8480321)

v0.1.0 (2024-07-18)

Unknown

  • Generators for BicvSplit rather than lists, reduce memory for large inputs. (4cd269c)

  • Change default plot behaviour for decomposition save. (0669dd7)

  • Amend nextflow docs (b749d8e)

  • Relative dir for slurm env.yaml (0af5f82)

  • Nextflow documentation (5e47929)

  • Documentation formatting updates (8fcab72)

  • Minor fix: nan suggested rank in plot (6d8634f)

  • Fix for docs: add furo to reqs. (ac4a5e2)

  • Docstyle update (b37cfd5)

  • Command line docs update (40c5b02)

  • Install instructions (c49ef86)

  • Extract alpha suggestion to function (7e8a76c)

  • Fix rank selection plot when no elbow detected (c156f7d)

  • Significance annotation on metadata plots (d610cc8)

  • Automated elbow detection. (aaf1664)

  • Regularisation selection CLI (b9d0f4f)

  • Misc changes (2660120)

  • Doc build fixes? (774c80f)

  • Doc build fixes? (3191b94)

  • Doc build fixes? (7a9140c)

  • Doc build fixes? (be335d1)

  • Doc build fixes? (9181f34)

  • Add sphinx click (d964b65)

  • Doc build attempt (52c3e3a)

  • Merge pull request #3 from apduncan/reapply_refactor

Reapply updates, combine methods added, other changes (b497ee0)

  • Plotting improvement, scaling synth data. (0d3df67)

  • Univar tests, plotting, qol. (abe62ab)

  • Plotting improvements. (5fae847)

  • Add PCoA. Remove MDS. Tests. (7fd2999)

  • Regularisation selection (94141b7)

  • Additional work on combining (9a8a722)

  • Basic approach to combine models implemented. (fc582a7)

  • Bugfix: Do not summarise i (3220efd)

  • Prevent copies of X matrix in BicvResult (bca551a)

  • Passing test (e4b6f2b)

  • Passing test (29d7fa8)

  • Generalised. Import problems. (b694103)

  • Start generalising reapply (ab0f542)

  • Fix distutil? Shorten tests (3115785)

  • Allow manual (b318b1e)

  • Merge remote-tracking branch 'origin/main' (4850b22)

  • Merge pull request #2 from apduncan/package

Start CI impl (f8913c3)