diff --git a/.flake8 b/.flake8 index e5d73fb..32ceb28 100644 --- a/.flake8 +++ b/.flake8 @@ -1,3 +1,3 @@ [flake8] ignore = F401, E203, W503 -max-line-length = 100 \ No newline at end of file +max-line-length = 125 \ No newline at end of file diff --git a/pandasaurus_cxg/anndata_analyzer.py b/pandasaurus_cxg/anndata_analyzer.py new file mode 100644 index 0000000..a2960db --- /dev/null +++ b/pandasaurus_cxg/anndata_analyzer.py @@ -0,0 +1,152 @@ +from enum import Enum +import os +from typing import List + +import pandas as pd + +from pandasaurus_cxg.anndata_loader import AnndataLoader +from pandasaurus_cxg.schema.schema_loader import read_json_file + + +# Check if the DEBUG environment variable is set +debug_mode = os.getenv('DEBUG') + +class AnndataAnalyzer: + """ + A class for providing methods for different type of analysis in an AnnData object. + + Args: + file_path (str): The path to the AnnData file. + schema_path (str): The path to the schema file. + + Attributes: + _anndata_obs (pd.DataFrame): The observation data from the AnnData object. + _schema (dict): The schema data loaded from the schema file. + + """ + + def __init__(self, file_path: str, schema_path: str): + """ + Initializes an instance of the AnndataAnalyzer class. + + Args: + file_path (str): The path to the AnnData file. + schema_path (str): The path to the schema file. + + """ + self._anndata_obs = AnndataLoader.load_from_file(file_path).obs + self._schema = read_json_file(schema_path) + + def co_annotation_report(self): + """ + Generates a co-annotation report based on the provided schema. + + Examples: + | subclass.l3, dPT, cluster_matches, subclass.full, Degenerative Proximal Tubule Epithelial Cell + | subclass.l3, aTAL1, subcluster_of, subclass.full, Adaptive / Maladaptive / Repairing Thick Ascending Limb Cell + | class, epithelial cells, cluster_matches, cell_type, kidney collecting duct intercalated cell + + Returns: + pd.DataFrame: The co-annotation report. + + """ + free_text_cell_type = [key for key, value in self._schema.items() if value] + temp_result = [] + for field_name_2 in free_text_cell_type: + for field_name_1 in free_text_cell_type: + if ( + field_name_1 != field_name_2 + and field_name_1 in self._anndata_obs.columns + and field_name_2 in self._anndata_obs.columns + ): + co_oc = ( + self._anndata_obs[[field_name_1, field_name_2]] + .drop_duplicates() + .reset_index(drop=True) + ) + field_name_2_dict = ( + co_oc.groupby(field_name_2)[field_name_1].apply(list).to_dict() + ) + field_name_1_dict = ( + co_oc.groupby(field_name_1)[field_name_2].apply(list).to_dict() + ) + co_oc["predicate"] = co_oc.apply( + self._assign_predicate, + args=( + field_name_1, + field_name_2, + field_name_1_dict, + field_name_2_dict, + debug_mode, + ), + axis=1, + ) + + temp_result.extend(co_oc.to_dict(orient="records")) + + result = [ + [item for sublist in [[k, v] for k, v in record.items()] for item in sublist] + for record in temp_result + ] + unique_result = self._remove_duplicates(result) + return pd.DataFrame( + [inner_list[:2] + inner_list[5:6] + inner_list[2:4] for inner_list in unique_result], + columns=["field_name1", "value1", "predicate", "field_name2", "value2"], + ) + + + @staticmethod + def _remove_duplicates(data: List[List[str]]): + unique_data = [] + unique_set = set() + + for sublist in data: + if Predicate.SUPERCLUSTER_OF.value in sublist: + continue + sorted_sublist = tuple(sorted(set(sublist))) + if sorted_sublist not in unique_set: + unique_data.append(sublist) + unique_set.add(sorted_sublist) + return unique_data + + @staticmethod + def _assign_predicate( + row, field_name_1, field_name_2, field_name_1_dict, field_name_2_dict, debug + ): + if debug: + print("Debugging row:", row) + print("Value of field_name_1:", row[field_name_1]) + print("Value of field_name_1_dict:", field_name_1_dict.get(row[field_name_1], [])) + print("Value of field_name_2:", row[field_name_2]) + print("Value of field_name_2_dict:", field_name_2_dict.get(row[field_name_2], [])) + + field_name_1_values = field_name_1_dict.get(row[field_name_1], []) + field_name_2_values = field_name_2_dict.get(row[field_name_2], []) + + if field_name_2_dict.get(row[field_name_2], []) == [ + row[field_name_1] + ] and field_name_1_dict.get(row[field_name_1], []) == [row[field_name_2]]: + return Predicate.CLUSTER_MATCHES.value + + if ( + row[field_name_1] in field_name_2_values + and row[field_name_2] in field_name_1_values + and len(field_name_1_values) == 1 + ): + return Predicate.SUBCLUSTER_OF.value + + if ( + row[field_name_1] in field_name_2_values + and row[field_name_2] in field_name_1_values + and len(field_name_2_values) == 1 + ): + return Predicate.SUPERCLUSTER_OF.value + + return Predicate.CLUSTER_OVERLAPS.value + + +class Predicate(Enum): + CLUSTER_MATCHES = "cluster_matches" + CLUSTER_OVERLAPS = "cluster_overlaps" + SUBCLUSTER_OF = "subcluster_of" + SUPERCLUSTER_OF = "supercluster_of" diff --git a/pandasaurus_cxg/anndata_enricher.py b/pandasaurus_cxg/anndata_enricher.py index 03d8634..bcc1cc7 100644 --- a/pandasaurus_cxg/anndata_enricher.py +++ b/pandasaurus_cxg/anndata_enricher.py @@ -31,6 +31,7 @@ def __init__( The slim list is used in minimal_slim_enrichment and full_slim_enrichment. Defaults to "Cell Ontology" """ + # TODO Do we need to keep whole anndata? Would it be enough to keep the obs only? self._anndata = AnndataLoader.load_from_file(file_path) self.__seed_list = self._anndata.obs[cell_type_field].unique().tolist() self.__enricher = Query(self.__seed_list) diff --git a/pandasaurus_cxg/schema/__init__.py b/pandasaurus_cxg/schema/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/pandasaurus_cxg/schema/schema.json b/pandasaurus_cxg/schema/schema.json new file mode 100644 index 0000000..76e7e96 --- /dev/null +++ b/pandasaurus_cxg/schema/schema.json @@ -0,0 +1,61 @@ +{ + "nCount_RNA": false, + "nFeature_RNA": false, + "library": false, + "percent.er": false, + "percent.mt": false, + "degen.score": false, + "aEpi.score": false, + "aStr.score": false, + "cyc.score": false, + "matrisome.score": false, + "collagen.score": false, + "glycoprotein.score": false, + "proteoglycan.score": false, + "S.Score": false, + "G2M.Score": false, + "experiment": false, + "specimen": false, + "condition.long": false, + "condition.l1": false, + "condition.l2": false, + "donor_id": false, + "region.l1": false, + "region.l2": false, + "percent.cortex": false, + "percent.medulla": false, + "tissue_type": false, + "id": false, + "pagoda_k100_infomap_coembed": false, + "subclass.full": true, + "subclass.l3": true, + "subclass.l2": true, + "subclass.l1": true, + "state.l2": true, + "state": true, + "class": true, + "structure": false, + "disease_ontology_term_id": false, + "sex_ontology_term_id": false, + "development_stage_ontology_term_id": false, + "self_reported_ethnicity_ontology_term_id": false, + "eGFR": false, + "BMI": false, + "diabetes_history": false, + "hypertension": false, + "tissue_ontology_term_id": false, + "organism_ontology_term_id": false, + "assay_ontology_term_id": false, + "cell_type_ontology_term_id": false, + "is_primary_data": false, + "suspension_type": false, + "cell_type": true, + "assay": false, + "disease": false, + "organism": false, + "sex": false, + "tissue": false, + "self_reported_ethnicity": false, + "development_stage": false, + "author_cell_type": true +} \ No newline at end of file diff --git a/pandasaurus_cxg/schema/schema_loader.py b/pandasaurus_cxg/schema/schema_loader.py new file mode 100644 index 0000000..6345f29 --- /dev/null +++ b/pandasaurus_cxg/schema/schema_loader.py @@ -0,0 +1,7 @@ +import json + + +def read_json_file(file_path): + with open(file_path, "r") as file: + json_data = json.load(file) + return json_data diff --git a/poetry.lock b/poetry.lock index a00188b..26220a4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -123,13 +123,13 @@ lxml = ["lxml"] [[package]] name = "bioregistry" -version = "0.9.38" +version = "0.9.53" description = "Integrated registry of biological databases and nomenclatures" optional = false python-versions = ">=3.7" files = [ - {file = "bioregistry-0.9.38-py3-none-any.whl", hash = "sha256:e9ffda66a3a5f04c93b78e45b28a14b5f5bc4f04e41ef52701a044f781d4e4e3"}, - {file = "bioregistry-0.9.38.tar.gz", hash = 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"flake8-requirements", "flake8-typechecking-import", "flake8-use-fstring", "mypy", "pep8-naming", "types-PyYAML"] [[package]] name = "url-normalize" @@ -3300,4 +3293,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "cefb11122a57f16b6ad614390db5a0efd6b0d5d06ff2b86e97b7010b7408f9e8" +content-hash = "953efd0b9f796ff8b92b8f9b53255c7e4dc25b18f1a58e83722f53eb7a74f7f4" diff --git a/pyproject.toml b/pyproject.toml index a298bdf..1b0178c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ packages = [{include = "pandasaurus_cxg"}] [tool.poetry.dependencies] python = "^3.9" pandas = "^2.0.2" -pandasaurus = "0.1.0" +pandasaurus = "0.2.2" anndata = "^0.9.1" [tool.poetry.group.dev.dependencies] diff --git a/walkthrough.ipynb b/walkthrough.ipynb new file mode 100644 index 0000000..8784094 --- /dev/null +++ b/walkthrough.ipynb @@ -0,0 +1,243 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Pandasaurus CxG Extension Walkthrough " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Overview\n", + "Welcome to this Jupyter notebook walkthrough for pandasaurus_cxg! This library provides powerful tools for analyzing and enriching AnnData objects, enabling you to gain deeper insights into your single-cell RNA sequencing (scRNA-seq) data.\n", + "\n", + "In this notebook, we will explore two main classes: `AnndataEnricher` and `AnndataAnalyzer`. Let's dive in and see how these classes can help us in our scRNA-seq analysis.\n", + "\n", + "Now, let's get started with an example workflow that demonstrates the capabilities of these classes. We'll load an example dataset, perform enrichment, analysis, and visualization steps to gain a better understanding of our scRNA-seq data.\n", + "\n", + "Let's import the necessary modules and get started!" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Requirement already satisfied: oaklib==0.5.12 in ./venv/lib/python3.9/site-packages (0.5.12)\n", + "Requirement already satisfied: SPARQLWrapper in ./venv/lib/python3.9/site-packages (from oaklib==0.5.12) (2.0.0)\n", + "Requirement already satisfied: SQLAlchemy>=1.4.32 in ./venv/lib/python3.9/site-packages (from oaklib==0.5.12) (2.0.16)\n", + "Requirement already satisfied: airium>=0.2.5 in ./venv/lib/python3.9/site-packages (from oaklib==0.5.12) (0.2.5)\n", + "Requirement already satisfied: appdirs>=1.4.4 in ./venv/lib/python3.9/site-packages (from oaklib==0.5.12) (1.4.4)\n", + "Requirement already 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"!pip install -i https://test.pypi.org/simple/ pandasaurus==0.2.0" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "ename": "ModuleNotFoundError", + "evalue": "No module named 'src'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[4], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpandasaurus_cxg\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01manndata_enricher\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m AnndataEnricher\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpandasaurus_cxg\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01manndata_analyzer\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m AnndataAnalyzer\n", + "File \u001b[0;32m~/github/pandasaurus_cxg/pandasaurus_cxg/anndata_enricher.py:4\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mtyping\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m List, Optional\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mpandas\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mpd\u001b[39;00m\n\u001b[0;32m----> 4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpandasaurus\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mquery\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Query\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpandasaurus\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mslim_manager\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SlimManager\n\u001b[1;32m 7\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpandasaurus_cxg\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01manndata_loader\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m AnndataLoader\n", + "File \u001b[0;32m~/github/pandasaurus_cxg/venv/lib/python3.9/site-packages/pandasaurus/query.py:6\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mtyping\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m List, Optional\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mpandas\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mpd\u001b[39;00m\n\u001b[0;32m----> 6\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01msrc\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpandasaurus\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcurie_validator\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m CurieValidator\n\u001b[1;32m 7\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01msrc\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpandasaurus\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mresources\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mterm\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Term\n\u001b[1;32m 8\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01msrc\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpandasaurus\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mslim_manager\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SlimManager\n", + "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'src'" + ] + } + ], + "source": [ + "from pandasaurus_cxg.anndata_enricher import AnndataEnricher\n", + "from pandasaurus_cxg.anndata_analyzer import AnndataAnalyzer" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.16" + } + }, + "nbformat": 4, + "nbformat_minor": 1 +}