From b3cf832a4177cc1b4decdc1a53347aa431f0ea4f Mon Sep 17 00:00:00 2001 From: Ismail Ugur Bayindir Date: Thu, 28 Nov 2024 10:22:06 +0000 Subject: [PATCH] Add number of cells to each cell set node (#91) * Update version to 0.2.2 * Refactor co_annotation_report by introducing _generate_co_annotation_dataframe * Add cell_count to cell sets * Update test_graph_generator.py --- pandasaurus_cxg/anndata_analyzer.py | 49 +- .../graph_generator/graph_generator.py | 2 +- poetry.lock | 1755 +++++++++++------ pyproject.toml | 2 +- test/graph_generator/test_graph_generator.py | 12 +- 5 files changed, 1159 insertions(+), 661 deletions(-) diff --git a/pandasaurus_cxg/anndata_analyzer.py b/pandasaurus_cxg/anndata_analyzer.py index 5692d3f..d9a102d 100644 --- a/pandasaurus_cxg/anndata_analyzer.py +++ b/pandasaurus_cxg/anndata_analyzer.py @@ -89,7 +89,9 @@ def from_file_path(file_path: str, author_cell_type_list: Optional[List[str]] = """ return AnndataAnalyzer(AnndataLoader.load_from_file(file_path), author_cell_type_list) - def co_annotation_report(self, disease: Optional[str] = None, enrich: bool = False): + def co_annotation_report( + self, disease: Optional[str] = None, enrich: bool = False + ) -> pd.DataFrame: """ Generates a co-annotation report based on the provided schema. @@ -103,7 +105,23 @@ def co_annotation_report(self, disease: Optional[str] = None, enrich: bool = Fal Returns: pd.DataFrame: The co-annotation report. + """ + # Call the core method to generate the full DataFrame + full_df = self._generate_co_annotation_dataframe(disease, enrich) + + # Return only the first 5 columns + return full_df.iloc[:, :5] + def _generate_co_annotation_dataframe(self, disease: Optional[str] = None, enrich: bool = False): + """ + Core method to generate a full co-annotation dataframe. + + Args: + disease (Optional[str]): A valid disease CURIE used to filter the rows. + enrich (bool): Whether to enable enrichment in the co-annotation report. + + Returns: + pd.DataFrame: The complete co-annotation dataframe with all columns. """ # TODO needs a refactoring about what enrichment method to use. Or would it better to accept # enriched_df as parameter, so users get to decide? @@ -136,6 +154,16 @@ def co_annotation_report(self, disease: Optional[str] = None, enrich: bool = Fal ).reset_index(drop=True) AnndataAnalyzer._assign_predicate_column(co_oc, field_name_1, field_name_2) + # Calculate cell counts for `field_name_1` + field_1_counts = ( + self._anndata.obs.groupby(field_name_1, observed=False).size().to_dict() + ) + co_oc[f"{field_name_1}_cell_count"] = co_oc[field_name_1].map(field_1_counts) + # Calculate cell counts for `field_name_2` + field_2_counts = ( + self._anndata.obs.groupby(field_name_2, observed=False).size().to_dict() + ) + co_oc[f"{field_name_2}_cell_count"] = co_oc[field_name_2].map(field_2_counts) temp_result.extend(co_oc.to_dict(orient="records")) result = [ @@ -144,8 +172,23 @@ def co_annotation_report(self, disease: Optional[str] = None, enrich: bool = Fal ] # unique_result = AnndataAnalyzer._remove_duplicates(result) self.report_df = pd.DataFrame( - [inner_list[:2] + inner_list[5:6] + inner_list[2:4] for inner_list in result], - columns=["field_name1", "value1", "predicate", "field_name2", "value2"], + [ + inner_list[:2] + + inner_list[5:6] + + inner_list[2:4] + + inner_list[7:8] + + inner_list[9:10] + for inner_list in result + ], + columns=[ + "field_name1", + "value1", + "predicate", + "field_name2", + "value2", + "field_name1_cell_count", + "field_name2_cell_count", + ], ) return self.report_df diff --git a/pandasaurus_cxg/graph_generator/graph_generator.py b/pandasaurus_cxg/graph_generator/graph_generator.py index 6a3ff56..ab9bee0 100644 --- a/pandasaurus_cxg/graph_generator/graph_generator.py +++ b/pandasaurus_cxg/graph_generator/graph_generator.py @@ -100,7 +100,7 @@ def generate_rdf_graph(self, merge: bool = False): temp_dict = {} for inner_list in inner_dict.values.tolist(): # Initialize the base dictionary based on the current list - inner_dict_uuid = {inner_list[0]: inner_list[1]} + inner_dict_uuid = {inner_list[0]: inner_list[1], "cell_count": inner_list[5]} # Update dictionary based on specific conditions if inner_list[2] == "subcluster_of": diff --git a/poetry.lock b/poetry.lock index 8a42f8b..3dfe4fe 100644 --- a/poetry.lock +++ b/poetry.lock @@ -89,13 +89,13 @@ files = [ [[package]] name = "array-api-compat" -version = "1.9" +version = "1.9.1" description = "A wrapper around NumPy and other array libraries to make them compatible with the Array API standard" optional = false -python-versions = "*" +python-versions = ">=3.9" files = [ - {file = "array_api_compat-1.9-py3-none-any.whl", hash = "sha256:76db63c2d2461ba0e86b920c8b087f0a1617eb14de3ec29fe6811eeecad9c5e8"}, - {file = "array_api_compat-1.9.tar.gz", hash = "sha256:8fb35f2895822b1cc6618449efd84aa76dcea1ab96940304f869663fd6a0dcd8"}, + {file = "array_api_compat-1.9.1-py3-none-any.whl", hash = "sha256:41a2703a662832d21619359ddddc5c0449876871f6c01e108c335f2a9432df94"}, + {file = "array_api_compat-1.9.1.tar.gz", hash = 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graph_generator = graph_generator_instance_for_kidney graph_generator.generate_rdf_graph(merge=True) - assert len(graph_generator.graph) == 648 + assert len(graph_generator.graph) == 743 assert ( len([[s, p, o] for s, p, o in graph_generator.graph.triples((None, RDF.type, None))]) == 146 ) @@ -132,7 +132,7 @@ def test_generate_rdf_graph_with_merge(graph_generator_instance_for_kidney): def test_generate_rdf_graph_without_merge(graph_generator_instance_for_kidney): graph_generator = graph_generator_instance_for_kidney graph_generator.generate_rdf_graph() - assert len(graph_generator.graph) == 1912 + assert len(graph_generator.graph) == 2173 assert ( len([[s, p, o] for s, p, o in graph_generator.graph.triples((None, RDF.type, None))]) == 312 ) @@ -161,11 +161,11 @@ def test_enrich_rdf_graph_with_merge(graph_generator_instance_for_kidney): graph_generator = graph_generator_instance_for_kidney graph_generator.generate_rdf_graph(merge=True) - assert len(graph_generator.graph) == 648 + assert len(graph_generator.graph) == 743 graph_generator.enrich_rdf_graph() - assert len(graph_generator.graph) == 1147 + assert len(graph_generator.graph) == 1242 assert ( URIRef(CONSIST_OF.get("iri")), RDFS.label, @@ -190,11 +190,11 @@ def test_enrich_rdf_graph_without_merge(graph_generator_instance_for_kidney): graph_generator = graph_generator_instance_for_kidney graph_generator.generate_rdf_graph() - assert len(graph_generator.graph) == 1912 + assert len(graph_generator.graph) == 2173 graph_generator.enrich_rdf_graph() - assert len(graph_generator.graph) == 2411 + assert len(graph_generator.graph) == 2672 def test_save_rdf_graph(graph_generator_instance_for_kidney):