.. _api: API === Import scirpy together with scanpy as .. code-block:: python import scanpy as sc import scirpy as ir For consistency, the scirpy API tries to follow the `scanpy API `__ as closely as possible. .. _api-io: Input/Output: `io` ------------------ .. module:: scirpy.io .. currentmodule:: scirpy .. note:: **scirpy's data structure has been updated in v0.13.0.** Previously, receptor data was expanded into columns of `adata.obs`, now they are stored as an :term:`awkward array` in `adata.obsm["airr"]`. Moreover, we now use :class:`~mudata.MuData` to handle paired transcriptomics and :term:`AIRR` data. :class:`~anndata.AnnData` objects created with older versions of scirpy can be upgraded with :func:`scirpy.io.upgrade_schema` to be compatible with the latest version of scirpy. Please check out * the `release notes `_ for details about the changes and * the documentation about :ref:`Scirpy's data structure ` .. autosummary:: :toctree: ./generated io.upgrade_schema The following functions allow to import :term:`V(D)J` information from various formats. .. autosummary:: :toctree: ./generated io.read_h5mu io.read_h5ad io.read_10x_vdj io.read_tracer io.read_bracer io.read_bd_rhapsody io.read_airr io.from_dandelion Scirpy can export data to the following formats: .. autosummary:: :toctree: ./generated io.write_airr io.to_dandelion To convert own formats into the scirpy :ref:`data-structure`, we recommend building a list of :class:`~scirpy.io.AirrCell` objects first, and then converting them into an :class:`~anndata.AnnData` object using :func:`~scirpy.io.from_airr_cells`. For more details, check the :ref:`Data loading tutorial `. .. autosummary:: :toctree: ./generated io.AirrCell io.from_airr_cells io.to_airr_cells Preprocessing: `pp` ------------------- .. module:: scirpy.pp .. currentmodule:: scirpy .. autosummary:: :toctree: ./generated pp.index_chains pp.merge_airr pp.ir_dist Get: `get` ---------- The `get` module allows retrieving :term:`AIRR` data stored in `adata.obsm["airr"]` as a per-cell :class:`~pandas.DataFrame` or :class:`~pandas.Series`. .. module:: scirpy.get .. currentmodule:: scirpy .. autosummary:: :toctree: ./generated get.airr get.obs_context get.airr_context Tools: `tl` ----------- .. module:: scirpy.tl .. currentmodule:: scirpy Tools add an interpretable annotation to the :class:`~anndata.AnnData` object which usually can be visualized by a corresponding plotting function. Generic ^^^^^^^ .. autosummary:: :toctree: ./generated tl.group_abundance Quality control ^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated tl.chain_qc Define and visualize clonotypes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated tl.define_clonotypes tl.define_clonotype_clusters tl.clonotype_convergence tl.clonotype_network tl.clonotype_network_igraph Analyse clonal diversity ^^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated tl.clonal_expansion tl.summarize_clonal_expansion tl.alpha_diversity tl.repertoire_overlap tl.clonotype_modularity tl.clonotype_imbalance Query reference databases ^^^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated tl.ir_query tl.ir_query_annotate tl.ir_query_annotate_df V(D)J gene usage ^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated tl.spectratype Calculating mutations ^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated tl.mutational_load Plotting: `pl` -------------- .. module:: scirpy.pl .. currentmodule:: scirpy Generic ^^^^^^^ .. autosummary:: :toctree: ./generated pl.embedding Tools ^^^^^ Every of these plotting functions has a corresponding *tool* in the :mod:`scirpy.tl` section. Depending on the computational load, tools are either invoked on-the-fly when calling the plotting function or need to be precomputed and stored in :class:`~anndata.AnnData` previously. .. autosummary:: :toctree: ./generated pl.alpha_diversity pl.clonal_expansion pl.group_abundance pl.spectratype pl.vdj_usage pl.repertoire_overlap pl.clonotype_modularity pl.clonotype_network pl.clonotype_imbalance pl.logoplot_cdr3_motif Base plotting functions: `pl.base` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated pl.base.bar pl.base.line pl.base.barh pl.base.curve Plot styling: `pl.styling` ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated pl.styling.apply_style_to_axes pl.styling.style_axes Datasets: `datasets` -------------------- .. module:: scirpy.datasets .. currentmodule:: scirpy Example datasets ^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated datasets.wu2020 datasets.wu2020_3k datasets.maynard2020 datasets.stephenson2021_5k Reference databases ^^^^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated datasets.vdjdb datasets.iedb A reference database is also just a :ref:`Scirpy-formatted AnnData object`. This means you can follow the instructions in the :ref:`data loading tutorial ` to build a custom reference database. Utility functions: `util` ------------------------- .. module:: scirpy.util .. currentmodule:: scirpy .. autosummary:: :toctree: ./generated util.DataHandler util.graph.layout_components util.graph.layout_fr_size_aware util.graph.igraph_from_sparse_matrix IR distance utilities: `ir_dist` ----------------------------------- .. module:: scirpy.ir_dist .. currentmodule:: scirpy .. autosummary:: :toctree: ./generated ir_dist.sequence_dist distance metrics ^^^^^^^^^^^^^^^^ .. autosummary:: :toctree: ./generated ir_dist.metrics.DistanceCalculator ir_dist.metrics.ParallelDistanceCalculator ir_dist.metrics.IdentityDistanceCalculator ir_dist.metrics.LevenshteinDistanceCalculator ir_dist.metrics.HammingDistanceCalculator ir_dist.metrics.GPUHammingDistanceCalculator ir_dist.metrics.AlignmentDistanceCalculator ir_dist.metrics.FastAlignmentDistanceCalculator ir_dist.metrics.TCRdistDistanceCalculator