docs: more pedagogic tutorials for data_organization and condition_comparisons - #185
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saatvik-viniak wants to merge 27 commits into
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docs: more pedagogic tutorials for data_organization and condition_comparisons#185saatvik-viniak wants to merge 27 commits into
saatvik-viniak wants to merge 27 commits into
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…re functional now, more things to come soon.
…'stacked_violin' and scope='panel', the color bar will now show relative expression of a gene inside of its individual panel inside of the entire plot, thus it makes things easier in a sense for comparison qualitatively what gene is the highest expressed inside of a cluster.
…kal-Wallis, Dunn, Wilcoxon Signed Rank.
Hardening changes and doing some revisions for the non-parametric tests.
…statistical stacks
…d_getaffinity for darwin typeshed
… knobs; reuse validator checks persisted fingerprints; group mask preserves string categories
…lotlib, seaborn untouched)
…ependent fixtures
…e to statistic 0, p 1
- Corrected degenerate Welch/ANOVA and multiple-testing behavior. - Enforced valid sample-to-group and paired-study designs. - Honored metadata missing-value masks. - Prevented artifact-slot collisions from custom labels. - Added actual selected-value fingerprints, preventing stale statistical reuse after matrix changes. - Preserved immutable historical retrieval through exact ArtifactRefs. - Fixed NumPy sequence inputs. - Tightened plot/result compatibility across selections, groups, samples, pairs, normalization, and realized values. - Fixed shared-axis annotations, dark/custom themes, missing pairs, invalid subsets, infinite values, and invalid bracket heights. - Removed the plotting-to-datastore dependency and retained bounded per-feature fetching. Quality assessment
…hed NygenAnalytics#177) into stats_testing # Conflicts: # docs/source/tutorials/pseudobulk_and_differential_expression.md # scarf/datastore/_operations/features.py # scarf/datastore/_plot_accessor.py # scarf/features/statistical.py # scarf/metadata/arguments.py # scarf/plotting/distribution.py # tests/test_fate_helpers.py # tests/test_operation_argument_contracts.py # tests/test_plotting_modernization.py # tests/test_statistical.py # tests/test_statistical_datastore.py
…ndition testing tutorial
Reframe data_organization around checkpoints and revert boxes: Short Refresher with Scanpy/Seurat equivalents, live-I restore demos with update_key/reset_key/insert/drop, immutable-selection notes for filter_cells, and a revert cheat-sheet. Add a crash course on cell-specific stats testing to condition_comparisons, adapted to the donor-level paired design. Refresh the executed cache for the reworked data_organization page.
saatvik-viniak
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Makes two tutorials more intuitive and pedagogic (draft right now, slowly working on things).
data_organization was the first section
condition_comparisons was the second thing I focused on