Merge branch 'fix-445' into clonal-expansion

.pre-commit-config.yaml

@@ -26,7 +26,7 @@ repos:
         language_version: "17.9.1"
         exclude: '^\.conda'
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.1.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -10,14 +10,24 @@ and this project adheres to [Semantic Versioning][].
 
 ## [Unreleased]
 
+### Breaking changes
+
+-   Reimplement `pp.index_chains` using numba and awkward array functions, achieving a significant speedup. This function
+    behaves exactly like the previous version _except_ that callback functions passed to the `filter` arguments
+    must now be vectorized over an awkward array, e.g. to check if a `junction_aa` field is present you could
+    previously pass `lambda x: x['junction_aa'] is not None`, now an accepted version would be
+    `lambda x: ~ak.is_none(x["junction_aa"], axis=-1)`. To learn more about native awkward array functions, please
+    refer to the [awkward array documentation](https://awkward-array.org/doc/main/reference/index.html). ([#444](https://github.com/scverse/scirpy/pull/444))
+
 ### Additions
 
 -   The `clonal_expansion` function now supports a `breakpoints` argument for more flexible "expansion categories".
     The `breakpoints` argument supersedes the `clip_at` parameter, which is now deprecated. ([#439](https://github.com/scverse/scirpy/pull/439))
 
 ### Fixes
 
--   Fix that `define_clonotype_clusters` could not retrieve `within_group` columns from MuData ([#459](https://github.com/scverse/scirpy/pull/459))
+-   Fix that `define_clonotype_clusters` could not retreive `within_group` columns from MuData ([#459](https://github.com/scverse/scirpy/pull/459))
+-   Fix that AIRR Rearrangment fields of integer types could not be written when their value was None ([#465](https://github.com/scverse/scirpy/pull/465))
 
 ## v0.13.1
 

docs/tutorials/tutorial_3k_tcr.ipynb

@@ -3537,7 +3537,7 @@
    "notebook_metadata_filter": "-kernelspec"
   },
   "kernelspec": {
-   "display_name": "scirpy_dev2",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -3551,7 +3551,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,

src/scirpy/io/_io.py

@@ -584,9 +584,9 @@ def write_airr(adata: DataHandler.TYPE, filename: Union[str, Path], **kwargs) ->
     for tmp_cell in airr_cells:
         for chain in tmp_cell.to_airr_records():
             # workaround for AIRR library writing out int field as floats (if it happens to be a float)
-            for f in chain:
-                if RearrangementSchema.type(f) == "integer":
-                    chain[f] = int(chain[f])
+            for field, value in chain.items():
+                if RearrangementSchema.type(field) == "integer" and value is not None:
+                    chain[field] = int(value)
             writer.write(chain)
     writer.close()
 

src/scirpy/pp/_index_chains.py

@@ -1,19 +1,25 @@
+import operator
 from collections.abc import Mapping, Sequence
-from functools import partial
+from functools import partial, reduce
 from types import MappingProxyType
 from typing import Any, Callable, Union
 
 import awkward as ak
+import numba as nb
+import numpy as np
 from scanpy import logging
 
 from scirpy.io._datastructures import AirrCell
 from scirpy.util import DataHandler, _is_na2, tqdm
 
 SCIRPY_DUAL_IR_MODEL = "scirpy_dual_ir_v0.13"
+# make these constants available to numba
+_VJ_LOCI = tuple(AirrCell.VJ_LOCI)
+_VDJ_LOCI = tuple(AirrCell.VDJ_LOCI)
 
 
 @DataHandler.inject_param_docs()
-def index_chains(
+def index_chains_legacy(
     adata: DataHandler.TYPE,
     *,
     filter: Union[Callable[[Mapping], bool], Sequence[Union[str, Callable[[Mapping], bool]]]] = (
@@ -135,7 +141,168 @@ def index_chains(
     }
 
 
-def _key_sort_chains(chains: list[Mapping], sort_chains_by: Mapping[str, Any], idx: int) -> Sequence:
+@DataHandler.inject_param_docs()
+def index_chains(
+    adata: DataHandler.TYPE,
+    *,
+    filter: Union[Callable[[ak.Array], bool], Sequence[Union[str, Callable[[ak.Array], bool]]]] = (
+        "productive",
+        "require_junction_aa",
+    ),
+    sort_chains_by: Mapping[str, Any] = MappingProxyType(
+        {"duplicate_count": 0, "consensus_count": 0, "junction": "", "junction_aa": ""}
+    ),
+    airr_mod: str = "airr",
+    airr_key: str = "airr",
+    key_added: str = "chain_indices",
+) -> None:
+    """\
+    Selects primary/secondary VJ/VDJ cells per chain according to the :ref:`receptor-model`.
+
+    This function iterates through all chains stored in the :term:`awkward array` in
+    `adata.obsm[airr_key]` and
+
+     * labels chains as primary/secondary VJ/VDJ chains
+     * labels cells as multichain cells
+
+    based on the expression level of the chains and the specified filtering option.
+    By default, non-productive chains and chains without a valid CDR3 amino acid sequence are filtered out.
+
+    Additionally, chains without a valid IMGT locus are always filtered out.
+
+    For more details, please refer to the :ref:`receptor-model` and the :ref:`data structure <data-structure>`.
+
+    Parameters
+    ----------
+    {adata}
+    filter
+        Option to filter chains. Can be either
+          * a callback function that takes the full awkward array with AIRR chains as input and returns
+            another awkward array that is a boolean mask which can be used to index the former.
+            (True to keep, False to discard)
+          * a list of "filtering presets". Possible values are `"productive"` and `"require_junction_aa"`.
+            `"productive"` removes non-productive chains and `"require_junction_aa"` removes chains that don't have
+            a CDR3 amino acid sequence.
+          * a list with a combination of both.
+
+        Multiple presets/functions are combined using `and`. Filtered chains do not count towards calling "multichain" cells.
+    sort_chains_by
+        A list of sort keys used to determine an ordering of chains. The chain with the highest value
+        of this tuple will be the primary chain, second-highest the secondary chain. If there are more chains, they
+        will not be indexed, and the cell receives the "multichain" flag.
+    {airr_mod}
+    {airr_key}
+    key_added
+        Key under which the chain indicies will be stored in `adata.obsm` and metadata will be stored in `adata.uns`.
+
+    Returns
+    -------
+    Nothing, but adds a dataframe to `adata.obsm[chain_indices]`
+    """
+    params = DataHandler(adata, airr_mod, airr_key)
+
+    # prepare filter functions
+    if isinstance(filter, Callable):
+        filter = [filter]
+    filter_presets = {
+        "productive": lambda x: x["productive"],
+        "require_junction_aa": lambda x: ~ak.is_none(x["junction_aa"], axis=-1),
+    }
+    filter = [filter_presets[f] if isinstance(f, str) else f for f in filter]
+
+    # only warn if those fields are in the key (i.e. this should give a warning if those are missing with
+    # default settings. If the user specifies their own dictionary, they are on their own)
+    if "duplicate_count" in sort_chains_by and "consensus_count" in sort_chains_by:
+        if "duplicate_count" not in params.airr.fields and "consensus_count" not in params.airr.fields:
+            logging.warning("No expression information available. Cannot rank chains by expression. ")  # type: ignore
+
+    if "locus" not in params.airr.fields:
+        raise ValueError("The scirpy receptor model requires a `locus` field to be specified in the AIRR data.")
+
+    airr = params.airr
+    logging.info("Filtering chains...")
+    # Get the numeric indices pre-filtering - these are the indices we need in the final output as
+    # .obsm["airr"] is and remains unfiltered.
+    airr_idx = ak.local_index(airr, axis=1)
+    # Filter out chains that do not match the filter criteria
+    # we need an initial value that selects all chains in case filter is an empty list
+    airr_idx = airr_idx[reduce(operator.and_, (f(airr) for f in filter), ak.ones_like(airr_idx, dtype=bool))]
+
+    res = {}
+    is_multichain = np.zeros(len(airr), dtype=bool)
+    for chain_type, locus_names in {"VJ": AirrCell.VJ_LOCI, "VDJ": AirrCell.VDJ_LOCI}.items():
+        logging.info(f"Indexing {chain_type} chains...")
+        # get the indices for all VJ / VDJ chains, respectively
+        idx = airr_idx[_awkward_isin(airr["locus"][airr_idx], locus_names)]
+
+        # Now we need to sort the chains by the keys specified in `sort_chains_by`.
+        # since `argsort` doesn't support composite keys, we take advantage of the
+        # fact that the sorting algorithm is stable and sort the same array several times,
+        # starting with the lowest priority key up to the highest priority key.
+        for k, default in reversed(sort_chains_by.items()):
+            # skip this round of sorting altogether if field not present
+            if k in airr.fields:
+                logging.debug(f"Sorting chains by {k}")
+                tmp_idx = ak.argsort(ak.fill_none(airr[k][idx], default), stable=True, axis=-1, ascending=False)
+                idx = idx[tmp_idx]
+            else:
+                logging.debug(f"Skip sorting by {k} because field not present")
+
+        # We want the result to be lists of exactly 2 - clip if longer, pad with None if shorter.
+        res[chain_type] = ak.pad_none(idx, 2, axis=1, clip=True)
+        is_multichain |= ak.to_numpy(_awkward_len(idx)) > 2
+
+    # build results
+    logging.info("build result array")
+    res["multichain"] = is_multichain
+
+    params.adata.obsm[key_added] = ak.zip(res, depth_limit=1)  # type: ignore
+
+    # store metadata in .uns
+    params.adata.uns[key_added] = {
+        "model": SCIRPY_DUAL_IR_MODEL,  # can be used to distinguish different receptor models that may be added in the future.
+        "filter": str(filter),
+        "airr_key": airr_key,
+        "sort_chains_by": str(sort_chains_by),
+    }
+
+
+@nb.njit
+def _awkward_len_inner(arr, ab):
+    for row in arr:
+        ab.append(len(row))
+    return ab
+
+
+def _awkward_len(arr):
+    return _awkward_len_inner(arr, ak.ArrayBuilder()).snapshot()
+
+
+@nb.njit()
+def _awkward_isin_inner(arr, haystack, ab):
+    for row in arr:
+        ab.begin_list()
+        for v in row:
+            ab.append(v in haystack)
+        ab.end_list()
+    return ab
+
+
+def _awkward_isin(arr, haystack):
+    haystack = tuple(haystack)
+    return _awkward_isin_inner(arr, haystack, ak.ArrayBuilder()).snapshot()
+
+
+# For future reference, here would be two alternative implementations that are a bit
+# slower, but work without the need for numba.
+# def _awkward_len(arr):
+#     return ak.max(ak.local_index(arr, axis=1), axis=1)
+#
+# def _awkward_isin(arr, haystack):
+#     return reduce(operator.or_, (arr == el for el in haystack))
+
+
+def _key_sort_chains(chains, sort_chains_by: Mapping[str, Any], idx: int) -> Sequence:
     """Get key to sort chains by expression.
 
     Parameters

src/scirpy/tests/test_io.py

@@ -236,6 +236,15 @@ def test_airr_roundtrip_conversion(anndata_from_10x_sample, tmp_path):
     pdt.assert_frame_equal(anndata.obs, anndata2.obs, check_dtype=False, check_categorical=False)
 
 
+def test_write_airr_none_field_issue_454(tmp_path):
+    cell = AirrCell("cell1")
+    chain = cell.empty_chain_dict()
+    chain["d_sequence_end"] = None
+    cell.add_chain(chain)
+    adata = from_airr_cells([cell])
+    write_airr(adata, tmp_path / "test.airr.tsv")
+
+
 @pytest.mark.extra
 @pytest.mark.parametrize(
     "anndata_from_10x_sample",

src/scirpy/tests/test_plotting.py

@@ -16,6 +16,13 @@ def test_clonal_expansion(adata_clonotype):
     assert isinstance(p, plt.Axes)
 
 
+@pytest.mark.parametrize("adata_clonotype", [True], indirect=["adata_clonotype"], ids=["MuData"])
+def test_clonal_expansion_mudata_prefix(adata_clonotype):
+    """Regression test for #445"""
+    p = pl.clonal_expansion(adata_clonotype, groupby="group", target_col="airr:clone_id")
+    assert isinstance(p, plt.Axes)
+
+
 def test_alpha_diversity(adata_diversity):
     p = pl.alpha_diversity(adata_diversity, groupby="group", target_col="clonotype_")
     assert isinstance(p, plt.Axes)