diff --git a/_modules/pandasaurus_cxg/anndata_analyzer.html b/_modules/pandasaurus_cxg/anndata_analyzer.html index 5d9cb2b..cde64ec 100644 --- a/_modules/pandasaurus_cxg/anndata_analyzer.html +++ b/_modules/pandasaurus_cxg/anndata_analyzer.html @@ -222,9 +222,9 @@

Source code for pandasaurus_cxg.anndata_analyzer

[item for sublist in [[k, v] for k, v in record.items()] for item in sublist] for record in temp_result ] - unique_result = AnndataAnalyzer._remove_duplicates(result) + # 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 unique_result], + [inner_list[:2] + inner_list[5:6] + inner_list[2:4] for inner_list in result], columns=["field_name1", "value1", "predicate", "field_name2", "value2"], ) return self.report_df
diff --git a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html index 6d972b9..58574fe 100644 --- a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html +++ b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html @@ -274,6 +274,70 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

self.graph += self.ea.enricher_manager.enricher.graph
+
+[docs] + def add_metadata_nodes(self, metadata_fields: List[str]): + """ + Add metadata nodes to an RDF graph based on the specified metadata fields. Each node represents a metadata + attribute, and edges connecting these metadata nodes to cell clusters indicate the percentage contribution + of each metadata to the cluster. + + This function modifies the internal state of the RDF graph by adding new nodes and edges. + + Args: + metadata_fields (List[str]): A list of metadata field names that exist in the schema and should be added + to the RDF graph as nodes. + + Returns: + + """ + obs = self.ea.enricher_manager.anndata.obs + # metadata field validation + # TODO schema should be involved + missing_fields = [field for field in metadata_fields if field not in obs.keys()] + if missing_fields: + raise KeyError(f"Missing metadata fields: {', '.join(missing_fields)}") + + author_cell_types = list(self.ea.analyzer_manager.all_cell_type_identifiers) + # remove 'cell_type' from all_cell_type_identifiers + author_cell_types.pop(-1) + # add an annotation property for percentage + percentage_annotation_property = self.ns["percentage"] + self.graph.add((percentage_annotation_property, RDF.type, OWL.AnnotationProperty)) + for metadata in metadata_fields: + for s, _, _ in self.graph.triples((None, RDF.type, URIRef(CLUSTER.get("iri")))): + for a_cell_type in author_cell_types: + literal = self.graph.value(subject=s, predicate=self.ns[a_cell_type]) + if literal is None: + continue + percentages = ( + obs[obs[a_cell_type] == str(literal)][metadata].value_counts(normalize=True) + * 100 + ).loc[lambda x: x != 0.0] + for label, percentage in percentages.items(): + annotated_target = self.graph.value( + predicate=RDFS.label, object=Literal(label) + ) + if annotated_target is None: + annotated_target = URIRef(self.ns[str(uuid.uuid4())]) + self.graph.add((annotated_target, RDF.type, self.ns[metadata])) + self.graph.add((annotated_target, RDFS.label, Literal(label))) + bnode_axiom = BNode() + self.graph.add((bnode_axiom, RDF.type, OWL.Axiom)) + self.graph.add((bnode_axiom, OWL.annotatedSource, s)) + self.graph.add( + (bnode_axiom, OWL.annotatedProperty, self.ns["has_" + metadata]) + ) + self.graph.add((bnode_axiom, OWL.annotatedTarget, annotated_target)) + self.graph.add( + ( + bnode_axiom, + percentage_annotation_property, + Literal("{:.2f}".format(percentage)), + ) + )
+ +
[docs] def save_rdf_graph( diff --git a/genindex.html b/genindex.html index 94be9a7..32200c9 100644 --- a/genindex.html +++ b/genindex.html @@ -98,16 +98,18 @@

_

A

    +
  • AnndataEnricher (class in pandasaurus_cxg.anndata_enricher) +
  • AnndataEnrichmentAnalyzer (class in pandasaurus_cxg.enrichment_analysis)
  • AnndataLoader (class in pandasaurus_cxg.utils.anndata_loader) diff --git a/objects.inv b/objects.inv index 16f5464..0d8c581 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/pandasaurus_cxg/graph_generator/graph_generator.html b/pandasaurus_cxg/graph_generator/graph_generator.html index 29f6e29..b0c5732 100644 --- a/pandasaurus_cxg/graph_generator/graph_generator.html +++ b/pandasaurus_cxg/graph_generator/graph_generator.html @@ -97,6 +97,22 @@

    Documentation class pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator(enrichment_analyzer: AnndataEnrichmentAnalyzer, keys: List[str] | None = None)[source]
    +
    +add_metadata_nodes(metadata_fields: List[str])[source]
    +

    Add metadata nodes to an RDF graph based on the specified metadata fields. Each node represents a metadata +attribute, and edges connecting these metadata nodes to cell clusters indicate the percentage contribution +of each metadata to the cluster.

    +

    This function modifies the internal state of the RDF graph by adding new nodes and edges.

    +
    +
    Parameters:
    +

    metadata_fields (List[str]) – A list of metadata field names that exist in the schema and should be added +to the RDF graph as nodes.

    +
    +
    +

    Returns:

    +
    + +
    enrich_rdf_graph()[source]

    Enrich RDF graph with enriched DataFrame from AnndataEnricher

    diff --git a/searchindex.js b/searchindex.js index 89dfb02..adca3b8 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Anndata Analyzer": [[2, "anndata-analyzer"]], "Anndata Enricher": [[3, "anndata-enricher"]], "Anndata Enrichment Analysis": [[4, "anndata-enrichment-analysis"]], "Anndata Loader": [[9, "anndata-loader"]], "Contents:": [[0, null], [7, null], [8, null], [11, null]], "Documentation": [[2, "documentation"], [3, "documentation"], [4, "documentation"], [5, "documentation"], [6, "documentation"], [9, "documentation"], [10, "module-pandasaurus_cxg.utils.exceptions"]], "Exception Module": [[10, "exception-module"]], "Functions": [[6, "module-pandasaurus_cxg.graph_generator.graph_generator_utils"]], "Graph Generator": [[5, "graph-generator"], [7, "graph-generator"]], "Graph Generator Utils": [[6, "graph-generator-utils"]], "Indices and tables": [[0, "indices-and-tables"], [8, "indices-and-tables"]], "Installation": [[1, 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