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Results

CyteType returns detailed annotations per cluster and stores them on your AnnData object.

Access Results

Using get_results() Method (Recommended)

The get_results() method is the recommended way to retrieve CyteType results. It provides intelligent result fetching with automatic fallback to API retrieval:

# Helper
results = annotator.get_results()

import json
results = json.loads(adata.uns["cytetype_results"]["result"])

Typical Fields (per cluster)

  • annotation: primary cell type
  • granularAnnotation: finer phenotype
  • cellState: state/activation/malignancy
  • ontologyTerm: Cell Ontology term (e.g., CL_0000127)
  • confidence: model-assessed confidence
  • supportingMarkers / conflictingMarkers
  • missingExpression / unexpectedExpression
  • corroboratingPapers: literature support

Example loop:

for ann in results["annotations"]:
    print(ann["clusterId"], ann["annotation"], ann["ontologyTerm"], ann["confidence"])

For end-to-end examples and reports, see Examples.