Skip to content

README.md

Latest commit

 

History

History
38 lines (33 loc) · 4.13 KB

README.md

File metadata and controls

38 lines (33 loc) · 4.13 KB
Raw

adata_science_tools docs

This directory holds module-level documentation for public adata_science_tools APIs.

Available pages

  • _IO.md: core dataset save and AnnData-to-DataFrame helpers used across the package.
  • _analytical_plots.md: precomputed Kaplan–Meier and continuous-effect renderers with auditable returned tables.
  • _column_plots.md: horizontal bar plots, log2 fold-change dotplots, and multi-panel composite figure builders.
  • _corr_dotplots.md: correlation scatterplots, subgroup fit overlays, and rank-comparison helpers.
  • _plotting_updates.md: additive plotting-roadmap controls and compatibility summary.
  • _tabular_plots.md: ranked waterfall, category composition, and supplied-residual diagnostic plots.
  • _datapoints.md: unpaired variable-level datapoint plots with obs/var filters, grouped variables, optional box/violin overlays, and metric legends.
  • _diff_test.md: differential testing across independent, paired, and nested paired group comparisons, including CSV-backed input workflows.
  • _expectation_based_covar_correction.md: expectation-model fitting, artifact export, prediction, regression-based correction, and residual or ratio transforms for AnnData objects.
  • _forest.md: single-effect forest plots for supplied coefficients, odds ratios, confidence intervals, and p-values.
  • _histograms.md: AnnData and wide-DataFrame histogram plotting with obs/var filters and subgroup overlays.
  • _longitudinal.md: multi-timepoint subject trajectories with exact/display values and auditable segments.
  • _meta_forest.md: precomputed meta-analysis forest rows with pooled diamonds, prediction intervals, study sizing, subgroup headings, and custom tables.
  • _metab_IO.md: Metabolon Excel ingestion, layer creation, optional metadata merge, and dataset export behavior.
  • _model_fit.md: OLS and MixedLM model-fitting APIs, summary-table schemas, filtering support, and model-spec sidecar behavior.
  • _paired_datapoints.md: paired ref/target or Pre/Post datapoint plots with obs/var filters, grouping, and a synthetic example image.
  • _plots.md: volcano plots, QQ plots for p-values, and paired time-series datapoint plots.
  • _plots_depreciated.md: legacy plotting APIs kept for backward compatibility, with preferred modern replacements.
  • plotting_gallery.md: deterministic visual examples for maintained, compatibility, and deprecated plotting renderers, with analysis provenance and known coverage limits.
  • _preprocessing.md: row-wise AnnData preprocessing helpers, including paired target-vs-reference transforms.
  • _row_plots.md: grouped bar-plus-swarm row layouts from plain DataFrame input.
  • _simulate_data.md: covariate-driven dataset simulation helpers plus the config-driven example workflow used in example_simulated_data/.
  • _somascan_IO.md: SomaScan .adat ingestion, sample-type cleanup, index normalization, and SomaScan-specific DataFrame export helpers.
  • _utils.md: plotting helper functions for previewing and optionally saving color palettes.
  • _venn_plots.md: Venn and enrichment-overlap utilities in the package directory that are not currently re-exported at the package top level.
  • palettes.md: named palette constants exposed as adata_science_tools.palettes.

Notes

  • These pages document the current implementation in adata_science_tools, not an earlier design draft.
  • The first source of truth for behavior is the code in _tools/, _io/, _simulate_data/, and the tests in tests/.
  • Within _plotting, direct regression coverage includes analytical, correlation, histogram, datapoint, paired-datapoint, tabular, longitudinal, forest, and meta-analysis forest plotting APIs.