vampire.anno.tl.haplotype_leiden

vampire.anno.tl.haplotype_leiden#

vampire.anno.tl.haplotype_leiden(adata, resolution=1.0, *, random_state=0, sort_by='sample_size', store_key='haplotype')[source]#

Cluster samples into haplotypes using Leiden on the fused graph.

Reads the fused connectivities built by haplotype_neighbor(), runs the Leiden algorithm, builds a consensus sequence for each detected cluster, and stores haplotype labels in adata.obs.

Parameters:

  • adata (AnnData) – Annotated data with fused connectivities.

  • resolution (float) – Leiden resolution parameter. Higher values yield more clusters.

  • random_state (int) – Random seed for Leiden.

  • sort_by (str) – How to order the resulting haplotype labels. "sample_size" (default) sorts by the number of samples in each cluster (largest → H1). "copy_number" sorts by the average non-gap motif count per cluster (largest → H1).

  • store_key (str) – Key prefix. Must match the value used in haplotype_neighbor().

Return type:

AnnData

Returns:

  • adata – Updated in-place with:

    • obs[f"{store_key}"] — haplotype labels (category)

    • uns[f"{store_key}_consensus"] — consensus per haplotype

    Examples

  • ——–

  • >>> import vampire as vp

  • >>> vp.anno.pl.set_default_plotstyle()

  • >>> adata = vp.datasets.wdr7_hprc()

  • >>> vp.anno.tl.sample_msa(adata)

  • >>> vp.anno.tl.haplotype_neighbor(adata, metrics=[“structural”, “composition”])

  • >>> vp.anno.tl.haplotype_leiden(

  • >>> adata,

  • >>> resolution = 1.0

  • >>> )

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