get_hpa_localisation
- Cluster.get_hpa_localisation(cluster_name='clustering_res0.5', thresh=1, max_num_channels=3, limit_to_groups=None, **kwargs)[source]
Query subcellular localisation for each cluster from Human Protein Atlas (https://www.proteinatlas.org).
Calculates cluster loadings and returns the subcellular localisations of the channels that are enriched for each cluster. Requires “hpa_gene_name” column in channel_metadata.csv file in DATA_DIR to map channel names to genes available in HPA.
- Parameters
cluster_name (str) – Clustering to calculate localisations for. Must exist already.
thresh (float) – Minimum z-scored intensity value of channel in cluster to be considered for HPA query. thresh=0 considers all enriched channel of this cluster
max_num_channels (int) – Maximal number of channels to be considered for HPA query. Channels with highest z-scored intensity value will be used. If None, all channels passing thresh will be used.
limit_to_groups (Mapping[str, str | list[str]] | None) – Dict with obs as keys and groups from obs as values, to subset data before calculating loadings.
kwargs (Any) – Keyword arguments for
campa.tl.query_hpa_subcellular_location().
- Returns
Results dictionary with clusters as keys, and return value from
campa.tl.query_hpa_subcellular_location()- Return type