stereoAlign.metrics.ari

stereoAlign.metrics.ari(adata, cluster_key, label_key, implementation=None)

Adjusted Rand Index

The adjusted rand index is a chance-adjusted rand index, which evaluates the pair-wise accuracy of clustering vs. ground truth label assignments. The score ranges between 0 and 1 with larger values indicating better conservation of the data-driven cell identity discovery after integration compared to annotated labels.

Parameters

adata:

anndata object with cluster assignments in adata.obs[cluster_key]

cluster_key:

string of column in adata.obs containing cluster assignments

label_key:

string of column in adata.obs containing labels

implementation:

if set to ‘sklearn’, uses sklearn’s implementation, otherwise native implementation is taken

This function can be applied to all integration output types. The adata must contain cluster assignments that are based off the knn graph given or derived from the integration method output.