- Add ps to nf container
(
a91da23)
Added 'ps' to Nextflow container, which is required for Nextflow to generate runtime and resource usage reports.
- Fix build trigger
(
a6d80a8)
Typo in actions for triggering PyPI build/deploy
Making it clearer that five_es reapply expects DataFrame, and will total sum scale data. Also bumped python to 3.12 for itertools.batched.
-
cell_example: Update figures to fit manuscript draft (
3427a96) -
README: Add references to readme (
1fdeb6d)
Added building and releasing to PyPI to github actions.
- denovo: Added plot of weight distribution for signatures
(
03556f0)
Gave Decomposition a plot_weight_distribution method, which produces a column plot of the feature
weights in the signature.
- denovo.signature_similarity: Fix rank 1 only behaviour
(
16278f5)
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.
Added post-hoc testing using Dunn's test to the univariate_tests method. This information is not
yet displayed in the default plots.
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.
- denovo: Sort values by rank in stability rank select
(
391a2fa)
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.
- denovo: Use online kneed
(
beaefae)
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.
- Add summaries
(
4b48520)
summaries for some module and overall package added.
- feat(stability): allow use of signature similarity as rank selection method.
- *****: Tidy loggers
(
d918057)
use module loggers rather than the global logging functions
- data: Include swimmer data
(
9ef625b)
added swimmer data to repo.
- denovo: Allow custom colours for group in relative weight plot
(
3cf28ee)
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.
- denovo: Change to star suggested rank/alpha
(
6a23b2d)
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.
- denovo: Improve handling rank 1 by stability
(
ac80647)
removes decompositions of rank 1 from calculation of stability based rank selection methods, as not meaningful.
-
denovo: Load from tar.gz properly (
8fd938e) -
denovo: Remove rank 1 from stability rank suggestion. (
1829a17) -
denovo: Use consistent colours for bicv measures (
bf8f91b)
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.
- *****: Micromamba troubleshooting, docstring
(
6bc8093)
Fix method to make conda available to nextflow when using micromamba. Update some docstring formating to prevent newlines. Add semantic versioning to dev dependencies.
- data: Data subpackage added
(
ec89c6b)
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.
- data: Nsclc example data and notebook added
(
010a8e5)
add case study on NSCLC atlas to documentation, and included data in the data module.
- denovo: Change plotting backend
(
b095e84)
change relative weight plot to use marsilea remove patchwork lib update plotnine to 0.13.6
- denovo: Plot_metadata now can include modelfit
(
36e1f7d)
add model fit to the standard metadata plots. this will eventually replace plot_modelfit, but for now both exists.
- denovo: Stability rank selection methods
(
c780607)
Add cophenetic correlation and dispersion coefficients for rank selection and associated plots.
- denovo: Stability rank suggestion
(
5447016)
add function to suggest ranks based on peaks for stability based measures (dispersion, cophenetic correlation)