mantispy.pl.dendrogram

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mantispy.pl.dendrogram#

mantispy.pl.dendrogram(adata, key='cluster', color_threshold=None, ax=None)[source]#

Draw the hierarchical clustering tree stored by cluster().

Parameters:

  • adata (AnnData) – Object holding the linkage matrix cluster() wrote with method="hierarchical".

  • key (str (default: 'cluster')) – The key_added that run used, whose summary (leaf labels and the chosen cut) is read from uns["mantispy"][key].

  • color_threshold (float | None (default: None)) – Height below which branches share a colour, marking the clusters. Defaults to the cut cluster() chose, or scipy’s own default when that run set the count directly.

  • ax (Axes | None (default: None)) – Axes to draw on, or None for a new figure.

Return type:

Axes

Returns:

The axes drawn on, holding the tree with the profiles as leaves and merge height on the y axis.

Raises:

KeyError – uns["mantispy"] holds no key + "_linkage" (the run used method="leiden", or none ran).

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