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Add parameters for linkage() #224

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Add parameters for linkage() #224

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9 changes: 7 additions & 2 deletions vitessce/data_utils/anndata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -235,7 +235,7 @@ def to_uint8(arr, norm_along=None):
return norm_arr.astype('u1')


def sort_var_axis(adata_X, orig_var_index, full_var_index=None):
def sort_var_axis(adata_X, orig_var_index, full_var_index=None, linkage_method="ward", linkage_metric="euclidean", optimal_ordering=False):
"""
Sort the var index by performing hierarchical clustering.

Expand All @@ -252,7 +252,12 @@ def sort_var_axis(adata_X, orig_var_index, full_var_index=None):
gexp_arr = to_dense(adata_X)

# Perform hierarchical clustering along the genes axis.
Z = scipy.cluster.hierarchy.linkage(gexp_arr.T, method="ward")
Z = scipy.cluster.hierarchy.linkage(
gexp_arr.T,
method=linkage_method,
metric=linkage_metric,
optimal_ordering=optimal_ordering,
)

# Get the hierarchy-based ordering of genes.
leaf_index_list = scipy.cluster.hierarchy.leaves_list(Z)
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