├── .codecov.yml ├── .cruft.json ├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── bug-report.yml │ ├── config.yml │ └── enhancement-request.yml ├── dependabot.yml ├── pull_request_template.md └── workflows │ ├── benchmark.yml │ ├── check-pr.yml │ ├── ci.yml │ └── publish.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .taplo.toml ├── .vscode ├── launch.json └── settings.json ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── benchmarks ├── README.md ├── asv.conf.json └── benchmarks │ ├── __init__.py │ ├── _utils.py │ ├── preprocessing_counts.py │ ├── preprocessing_log.py │ └── tools.py ├── biome.jsonc ├── ci └── scripts │ ├── low-vers.py │ └── towncrier_automation.py ├── docs ├── Makefile ├── _static │ └── img │ │ ├── Scanpy_Logo.svg │ │ ├── Scanpy_Logo_BrightFG.svg │ │ ├── Scanpy_Logo_RGB.png │ │ ├── ci_plot-view_attachment-tab.png │ │ ├── ci_plot-view_select-test.png │ │ ├── ci_plot-view_tests-tab.png │ │ ├── spatial-basic-analysis.png │ │ ├── stacked_violin_dotplot_matrixplot.png │ │ └── tutorials │ │ ├── 170430_krumsiek11 │ │ └── timeseries.png │ │ ├── 170505_seurat │ │ ├── NKG7.png │ │ ├── cell_types.png │ │ ├── filter_genes_dispersion.png │ │ ├── louvain.png │ │ └── violin.png │ │ ├── 170522_visualizing_one_million_cells │ │ └── tsne_1.3M.png │ │ ├── paga_paul15.png │ │ └── paga_planaria.png ├── _templates │ └── autosummary │ │ └── class.rst ├── api │ ├── classes.md │ ├── datasets.md │ ├── deprecated.md │ ├── experimental.md │ ├── get.md │ ├── index.md │ ├── io.md │ ├── metrics.md │ ├── plotting.md │ ├── preprocessing.md │ ├── queries.md │ ├── settings.md │ └── tools.md ├── basic_usage.md ├── community.md ├── conf.py ├── contributors.md ├── dev │ ├── ci.md │ ├── code.md │ ├── documentation.md │ ├── getting-set-up.md │ ├── index.md │ ├── release.md │ ├── testing.md │ └── versioning.md ├── ecosystem.md ├── extensions │ ├── autosummary_skip_deprecated.py │ ├── autosummary_skip_inherited.py │ ├── canonical_tutorial.py │ ├── debug_docstrings.py │ ├── function_images.py │ ├── git_ref.py │ ├── has_attr_test.py │ ├── param_police.py │ └── patch_myst_nb.py ├── external │ ├── exporting.md │ ├── index.md │ ├── plotting.md │ ├── preprocessing.md │ └── tools.md ├── how-to │ ├── cell-cycle.ipynb │ ├── index.md │ ├── knn-transformers.ipynb │ └── plotting-with-marsilea.ipynb ├── index.md ├── installation.md ├── matplotlibrc ├── news.md ├── references.bib ├── references.rst ├── release-notes │ ├── 0.1.0.md │ ├── 0.2.1.md │ ├── 0.2.9.md │ ├── 0.3.0.md │ ├── 0.3.2.md │ ├── 0.4.0.md │ ├── 0.4.2.md │ ├── 0.4.3.md │ ├── 0.4.4.md │ ├── 1.0.0.md │ ├── 1.1.0.md │ ├── 1.10.0.md │ ├── 1.10.1.md │ ├── 1.10.2.md │ ├── 1.10.3.md │ ├── 1.10.4.md │ ├── 1.11.0.md │ ├── 1.11.1.md │ ├── 1.11.2.md │ ├── 1.11.3.md │ ├── 1.11.4.md │ ├── 1.11.5.md │ ├── 1.12.0rc1.md │ ├── 1.2.0.md │ ├── 1.2.1.md │ ├── 1.3.1.md │ ├── 1.3.3.md │ ├── 1.3.4.md │ ├── 1.3.5.md │ ├── 1.3.6.md │ ├── 1.3.7.md │ ├── 1.3.8.md │ ├── 1.4.1.md │ ├── 1.4.2.md │ ├── 1.4.3.md │ ├── 1.4.4.md │ ├── 1.4.5.md │ ├── 1.4.6.md │ ├── 1.5.0.md │ ├── 1.5.1.md │ ├── 1.6.0.md │ ├── 1.7.0.md │ ├── 1.7.1.md │ ├── 1.7.2.md │ ├── 1.8.0.md │ ├── 1.8.1.md │ ├── 1.8.2.md │ ├── 1.9.0.md │ ├── 1.9.1.md │ ├── 1.9.2.md │ ├── 1.9.3.md │ ├── 1.9.4.md │ ├── 1.9.5.md │ ├── 1.9.6.md │ ├── 1.9.7.md │ ├── 1.9.8.md │ ├── 3675.misc.md │ ├── 3894.docs.md │ ├── 3896.docs.md │ └── index.md ├── tutorials │ ├── basics │ │ ├── clustering-2017.ipynb │ │ ├── clustering.ipynb │ │ ├── index.md │ │ └── integrating-data-using-ingest.ipynb │ ├── experimental │ │ ├── dask.ipynb │ │ ├── index.md │ │ └── pearson_residuals.ipynb │ ├── index.md │ ├── plotting │ │ ├── advanced.ipynb │ │ ├── core.ipynb │ │ └── index.md │ └── trajectories │ │ ├── index.md │ │ └── paga-paul15.ipynb └── usage-principles.md ├── hatch.toml ├── pyproject.toml ├── src ├── scanpy │ ├── __init__.py │ ├── __main__.py │ ├── _compat.py │ ├── _settings │ │ ├── __init__.py │ │ └── verbosity.py │ ├── _singleton.py │ ├── _types.py │ ├── _utils │ │ ├── __init__.py │ │ ├── _doctests.py │ │ └── random.py │ ├── cli.py │ ├── datasets │ │ ├── 10x_pbmc68k_reduced.h5ad │ │ ├── __init__.py │ │ ├── _datasets.py │ │ ├── _ebi_expression_atlas.py │ │ ├── _utils.py │ │ ├── krumsiek11.txt │ │ └── toggleswitch.txt │ ├── experimental │ │ ├── __init__.py │ │ ├── _docs.py │ │ └── pp │ │ │ ├── __init__.py │ │ │ ├── _highly_variable_genes.py │ │ │ ├── _normalization.py │ │ │ └── _recipes.py │ ├── external │ │ ├── __init__.py │ │ ├── exporting.py │ │ ├── pl.py │ │ ├── pp │ │ │ ├── __init__.py │ │ │ ├── _bbknn.py │ │ │ ├── _dca.py │ │ │ ├── _harmony_integrate.py │ │ │ ├── _hashsolo.py │ │ │ ├── _magic.py │ │ │ ├── _mnn_correct.py │ │ │ └── _scanorama_integrate.py │ │ └── tl │ │ │ ├── __init__.py │ │ │ ├── _harmony_timeseries.py │ │ │ ├── _palantir.py │ │ │ ├── _phate.py │ │ │ ├── _phenograph.py │ │ │ ├── _pypairs.py │ │ │ ├── _sam.py │ │ │ ├── _trimap.py │ │ │ └── _wishbone.py │ ├── get │ │ ├── __init__.py │ │ ├── _aggregated.py │ │ └── get.py │ ├── logging.py │ ├── metrics │ │ ├── __init__.py │ │ ├── _common.py │ │ ├── _gearys_c.py │ │ ├── _metrics.py │ │ └── _morans_i.py │ ├── neighbors │ │ ├── __init__.py │ │ ├── _backends │ │ │ ├── __init__.py │ │ │ ├── _common.py │ │ │ └── rapids.py │ │ ├── _common.py │ │ ├── _connectivity.py │ │ ├── _doc.py │ │ └── _types.py │ ├── plotting │ │ ├── __init__.py │ │ ├── _anndata.py │ │ ├── _baseplot_class.py │ │ ├── _docs.py │ │ ├── _dotplot.py │ │ ├── _easter_egg.py │ │ ├── _matrixplot.py │ │ ├── _preprocessing.py │ │ ├── _qc.py │ │ ├── _rcmod.py │ │ ├── _scrublet.py │ │ ├── _stacked_violin.py │ │ ├── _tools │ │ │ ├── __init__.py │ │ │ ├── paga.py │ │ │ └── scatterplots.py │ │ ├── _utils.py │ │ ├── dogplot_images │ │ │ ├── doggo_1.webp │ │ │ ├── doggo_2.webp │ │ │ └── doggo_3.webp │ │ └── palettes.py │ ├── preprocessing │ │ ├── __init__.py │ │ ├── _combat.py │ │ ├── _deprecated │ │ │ ├── __init__.py │ │ │ ├── highly_variable_genes.py │ │ │ └── sampling.py │ │ ├── _distributed.py │ │ ├── _docs.py │ │ ├── _highly_variable_genes.py │ │ ├── _normalization.py │ │ ├── _pca │ │ │ ├── __init__.py │ │ │ ├── _compat.py │ │ │ └── _dask.py │ │ ├── _qc.py │ │ ├── _recipes.py │ │ ├── _scale.py │ │ ├── _scrublet │ │ │ ├── __init__.py │ │ │ ├── core.py │ │ │ ├── pipeline.py │ │ │ └── sparse_utils.py │ │ ├── _simple.py │ │ └── _utils.py │ ├── queries │ │ ├── __init__.py │ │ └── _queries.py │ ├── readwrite.py │ ├── sim_models │ │ ├── __init__.py │ │ ├── krumsiek11.txt │ │ ├── krumsiek11_params.txt │ │ ├── toggleswitch.txt │ │ └── toggleswitch_params.txt │ └── tools │ │ ├── __init__.py │ │ ├── _dendrogram.py │ │ ├── _diffmap.py │ │ ├── _dpt.py │ │ ├── _draw_graph.py │ │ ├── _embedding_density.py │ │ ├── _ingest.py │ │ ├── _leiden.py │ │ ├── _louvain.py │ │ ├── _marker_gene_overlap.py │ │ ├── _paga.py │ │ ├── _rank_genes_groups.py │ │ ├── _score_genes.py │ │ ├── _sim.py │ │ ├── _tsne.py │ │ ├── _umap.py │ │ ├── _utils.py │ │ └── _utils_clustering.py └── testing │ └── scanpy │ ├── __init__.py │ ├── _helpers │ ├── __init__.py │ └── data.py │ └── _pytest │ ├── __init__.py │ ├── fixtures │ ├── __init__.py │ └── data.py │ ├── marks.py │ └── params.py └── tests ├── _data ├── 10x-10k-subset.zarr │ ├── .zgroup │ ├── X │ │ ├── .zarray │ │ ├── 0.0 │ │ ├── 1.0 │ │ ├── 2.0 │ │ ├── 3.0 │ │ └── 4.0 │ ├── obs │ │ ├── 0 │ │ └── .zarray │ └── var │ │ ├── 0 │ │ └── .zarray ├── 10x_data │ ├── 1.2.0 │ │ ├── filtered_gene_bc_matrices │ │ │ └── hg19_chr21 │ │ │ │ ├── barcodes.tsv │ │ │ │ ├── genes.tsv │ │ │ │ └── matrix.mtx │ │ ├── filtered_gene_bc_matrices_h5.h5 │ │ └── multiple_genomes.h5 │ └── 3.0.0 │ │ ├── filtered_feature_bc_matrix.h5 │ │ └── filtered_feature_bc_matrix │ │ ├── barcodes.tsv.gz │ │ ├── features.tsv.gz │ │ └── matrix.mtx.gz ├── cat_regressor_for_int_input.npy ├── objs_t_test.pkl ├── objs_wilcoxon.pkl ├── regress_test_small.npy ├── regress_test_small_cat.npy ├── score_genes_reference_paul2015.pkl └── visium_data │ ├── 1.0.0 │ ├── filtered_feature_bc_matrix.h5 │ └── spatial │ │ ├── scalefactors_json.json │ │ ├── tissue_hires_image.png │ │ ├── tissue_lowres_image.png │ │ └── tissue_positions_list.csv │ └── 2.1.0 │ └── raw_probe_bc_matrix.h5 ├── _images ├── 3dprojection │ └── expected.png ├── binary_pca │ └── expected.png ├── binary_pca_old │ └── expected.png ├── clustermap │ └── expected.png ├── clustermap_withcolor │ └── expected.png ├── correlation │ └── expected.png ├── dendrogram │ └── expected.png ├── dotplot │ └── expected.png ├── dotplot2 │ └── expected.png ├── dotplot3 │ └── expected.png ├── dotplot_dict │ └── expected.png ├── dotplot_gene_symbols │ └── expected.png ├── dotplot_groupby_index │ └── expected.png ├── dotplot_groupby_list_catorder │ └── expected.png ├── dotplot_obj │ └── expected.png ├── dotplot_obj_std_scale_group │ └── expected.png ├── dotplot_obj_std_scale_group_swap_axes │ └── expected.png ├── dotplot_obj_std_scale_var │ └── expected.png ├── dotplot_obj_std_scale_var_swap_axes │ └── expected.png ├── dotplot_obj_swap_axes │ └── expected.png ├── dotplot_std_scale_group │ └── expected.png ├── dotplot_totals │ └── expected.png ├── dpt_groups_pseudotime │ └── expected.png ├── dpt_timeseries │ └── expected.png ├── embedding-missing-values │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.False-legend.off-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.False-legend.off-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.False-legend.on_bottom-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.False-legend.on_bottom-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.False-legend.on_data-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.False-legend.on_data-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.False-legend.on_right-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.False-legend.on_right-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.True-legend.off-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.True-legend.off-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.True-legend.on_bottom-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.True-legend.on_bottom-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.True-legend.on_data-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.True-legend.on_data-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.True-legend.on_right-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.black_tup-na_in_legend.True-legend.on_right-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.False-legend.off-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.False-legend.off-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.False-legend.on_bottom-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.False-legend.on_bottom-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.False-legend.on_data-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.False-legend.on_data-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.False-legend.on_right-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.False-legend.on_right-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.True-legend.off-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.True-legend.off-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.True-legend.on_bottom-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.True-legend.on_bottom-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.True-legend.on_data-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.True-legend.on_data-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.True-legend.on_right-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[pca-na_color.default-na_in_legend.True-legend.on_right-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.off-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.off-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.on_bottom-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.on_bottom-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.on_data-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.on_data-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.on_right-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.on_right-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.off-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.off-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.on_bottom-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.on_bottom-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.on_data-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.on_data-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.on_right-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.on_right-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.False-legend.off-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.False-legend.off-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.False-legend.on_bottom-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.False-legend.on_bottom-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.False-legend.on_data-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.False-legend.on_data-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.False-legend.on_right-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.False-legend.on_right-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.True-legend.off-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.True-legend.off-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.True-legend.on_bottom-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.True-legend.on_bottom-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.True-legend.on_data-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.True-legend.on_data-groups.all] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.True-legend.on_right-groups.3] │ │ └── expected.png │ ├── test_missing_values_categorical[spatial-na_color.default-na_in_legend.True-legend.on_right-groups.all] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.black_tup-vbounds.default] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.black_tup-vbounds.norm] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.black_tup-vbounds.numbers] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.black_tup-vbounds.percentile] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.black_tup-vbounds.vcenter] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.default-vbounds.default] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.default-vbounds.norm] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.default-vbounds.numbers] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.default-vbounds.percentile] │ │ └── expected.png │ ├── test_missing_values_continuous[pca-na_color.default-vbounds.vcenter] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.black_tup-vbounds.default] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.black_tup-vbounds.norm] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.black_tup-vbounds.numbers] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.black_tup-vbounds.percentile] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.black_tup-vbounds.vcenter] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.default-vbounds.default] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.default-vbounds.norm] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.default-vbounds.numbers] │ │ └── expected.png │ ├── test_missing_values_continuous[spatial-na_color.default-vbounds.percentile] │ │ └── expected.png │ └── test_missing_values_continuous[spatial-na_color.default-vbounds.vcenter] │ │ └── expected.png ├── embedding_groups_size │ └── expected.png ├── embedding_outline_vmin_vmax │ └── expected.png ├── heatmap │ └── expected.png ├── heatmap2 │ └── expected.png ├── heatmap_gene_symbols │ └── expected.png ├── heatmap_small_alignment │ └── expected.png ├── heatmap_small_swap_alignment │ └── expected.png ├── heatmap_std_scale_obs │ └── expected.png ├── heatmap_std_scale_var │ └── expected.png ├── heatmap_swap_axes │ └── expected.png ├── heatmap_var_as_dict │ └── expected.png ├── highest_expr_genes │ └── expected.png ├── matrixplot │ └── expected.png ├── matrixplot2 │ └── expected.png ├── matrixplot_gene_symbols │ └── expected.png ├── matrixplot_std_scale_group │ └── expected.png ├── matrixplot_std_scale_var_dict │ └── expected.png ├── matrixplot_swap_axes │ └── expected.png ├── matrixplot_with_totals │ └── expected.png ├── multipanel │ └── expected.png ├── multipanel_vcenter │ └── expected.png ├── multiple_plots │ └── expected.png ├── no_colorbar │ └── expected.png ├── paga │ └── expected.png ├── paga_compare │ └── expected.png ├── paga_compare_continuous │ └── expected.png ├── paga_compare_pbmc3k │ └── expected.png ├── paga_compare_pca │ └── expected.png ├── paga_continuous │ └── expected.png ├── paga_continuous_multiple │ └── expected.png ├── paga_continuous_obs │ └── expected.png ├── paga_path │ └── expected.png ├── paga_pie │ └── expected.png ├── pca │ └── expected.png ├── pca_loadings │ └── expected.png ├── pca_loadings_10_points │ └── expected.png ├── pca_loadings_without_lowest │ └── expected.png ├── pca_marker_with_dimensions │ └── expected.png ├── pca_markers_colors_with_dimensions │ └── expected.png ├── pca_markers_with_dimensions │ └── expected.png ├── pca_mask │ └── expected.png ├── pca_multiple_markers_multiple_colors │ └── expected.png ├── pca_one_marker │ └── expected.png ├── pca_one_marker_multiple_colors │ └── expected.png ├── pca_sparse_layer │ └── expected.png ├── pca_with_fonts │ └── expected.png ├── ranked_genes │ └── expected.png ├── ranked_genes_dotplot │ └── expected.png ├── ranked_genes_dotplot_gene_names │ └── expected.png ├── ranked_genes_dotplot_logfoldchange │ └── expected.png ├── ranked_genes_dotplot_logfoldchange_vcenter │ └── expected.png ├── ranked_genes_heatmap │ └── expected.png ├── ranked_genes_heatmap_swap_axes │ └── expected.png ├── ranked_genes_heatmap_swap_axes_vcenter │ └── expected.png ├── ranked_genes_heatmap_swaped │ └── expected.png ├── ranked_genes_matrixplot │ └── expected.png ├── ranked_genes_matrixplot_gene_names_symbol │ └── expected.png ├── ranked_genes_matrixplot_n_genes_negative │ └── expected.png ├── ranked_genes_matrixplot_swap_axes │ └── expected.png ├── ranked_genes_matrixplot_swap_axes_vcenter │ └── expected.png ├── ranked_genes_sharey │ └── expected.png ├── ranked_genes_stacked_violin │ └── expected.png ├── ranked_genes_tracksplot │ └── expected.png ├── ranked_genes_violin │ └── expected.png ├── ranked_genes_violin_not_raw │ └── expected.png ├── scatter_AAAGCCTGGCTAAC-1_vs_AAATTCGATGCACA-1 │ └── expected.png ├── scatter_HES_percent_mito_bulk_labels │ └── expected.png ├── scatter_HES_percent_mito_n_genes │ └── expected.png ├── scatter_HES_percent_mito_n_genes_bulk_labels │ └── expected.png ├── scrublet │ └── expected.png ├── scrublet_no_threshold │ └── expected.png ├── scrublet_with_batches │ └── expected.png ├── spatial_external_img │ └── expected.png ├── spatial_general_cat │ └── expected.png ├── spatial_general_cont │ └── expected.png ├── spatial_general_nocol │ └── expected.png ├── spatial_visium │ └── expected.png ├── spatial_visium_default │ └── expected.png ├── spatial_visium_embedding │ └── expected.png ├── spatial_visium_empty_image │ └── expected.png ├── stacked_violin │ └── expected.png ├── stacked_violin_gene_symbols │ └── expected.png ├── stacked_violin_no_cat_obs │ └── expected.png ├── stacked_violin_return_fig │ └── expected.png ├── stacked_violin_std_scale_group │ └── expected.png ├── stacked_violin_std_scale_var_dict │ └── expected.png ├── stacked_violin_swap_axes_pbmc68k_reduced │ └── expected.png ├── stacked_violin_swapped_axes │ └── expected.png ├── tracksplot │ └── expected.png ├── tracksplot_gene_symbols │ └── expected.png ├── tsne │ └── expected.png ├── umap │ └── expected.png ├── umap_gene_expr │ └── expected.png ├── umap_layer │ └── expected.png ├── umap_nocolor │ └── expected.png ├── umap_symbols │ └── expected.png ├── umap_with_edges │ └── expected.png ├── violin_multi_panel │ └── expected.png ├── violin_multi_panel_with_groupby │ └── expected.png └── violin_multi_panel_with_layer │ └── expected.png ├── _scripts ├── cell_ranger_hvg.csv ├── scanpy-testbin ├── seurat_extract_hvg.r ├── seurat_extract_hvg_v3.r ├── seurat_hvg.csv ├── seurat_hvg_v3.csv.gz └── seurat_hvg_v3_batch.csv ├── conftest.py ├── external ├── test_harmony_integrate.py ├── test_harmony_timeseries.py ├── test_hashsolo.py ├── test_magic.py ├── test_palantir.py ├── test_phenograph.py ├── test_sam.py ├── test_scanorama_integrate.py └── test_wishbone.py ├── notebooks ├── _images_paga_paul15_subsampled │ ├── paga │ │ └── expected.png │ └── paga_path │ │ └── expected.png ├── _images_pbmc3k │ ├── filter_genes_dispersion │ │ └── expected.png │ ├── highest_expr_genes │ │ └── expected.png │ ├── pca │ │ └── expected.png │ ├── pca_variance_ratio │ │ └── expected.png │ ├── rank_genes_groups_1 │ │ └── expected.png │ ├── rank_genes_groups_2 │ │ └── expected.png │ ├── rank_genes_groups_3 │ │ └── expected.png │ ├── rank_genes_groups_4 │ │ └── expected.png │ ├── scatter_1 │ │ └── expected.png │ ├── scatter_2 │ │ └── expected.png │ ├── scatter_3 │ │ └── expected.png │ ├── violin │ │ └── expected.png │ └── violin_2 │ │ └── expected.png └── test_pbmc3k.py ├── test_aggregated.py ├── test_backed.py ├── test_binary.py ├── test_clustering.py ├── test_combat.py ├── test_datasets.py ├── test_dendrogram.py ├── test_deprecations.py ├── test_embedding.py ├── test_embedding_density.py ├── test_filter_rank_genes_groups.py ├── test_get.py ├── test_helpers.py ├── test_highly_variable_genes.py ├── test_ingest.py ├── test_logging.py ├── test_marker_gene_overlap.py ├── test_metrics.py ├── test_neighbors.py ├── test_neighbors_common.py ├── test_neighbors_key_added.py ├── test_normalization.py ├── test_package_structure.py ├── 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