UNAGI.marker_discovery.hierachical_static_markers.get_dataset_hcmarkers

UNAGI.marker_discovery.hierachical_static_markers.get_dataset_hcmarkers(adata, stage_key, cluster_key, use_rep, cutoff=0.05)[source]

Perform hierarchical clustering on the dataset and get the hierarchical clustering markers for each stage.

Parameters:

  • adata (AnnData) – The annotated data matrix.

  • stage_key (str) – The key of the stage information in adata.obs.

  • cluster_key (str) – The key of the cluster information in adata.obs.

  • use_rep (str) – The key of the representation in adata.obsm.

  • cutoff (float) – The cutoff of the adjusted p-value to select the hierarchical clustering markers. Default is 0.05.

Returns:

hcmarkers (dict) – The hierarchical clustering markers for each stage. The keys of the dictionary are the cluster information in adata.obs. The values of the dictionary are the positive and negative hierarchical clustering markers for each cluster. The positive and negative hierarchical clustering markers are pandas dataframe with the columns of the names of the genes, the log fold change and the adjusted p-value.