came.utils.plot.umap_with_annotates

came.utils.plot.umap_with_annotates(adt: AnnData, text_ids: Sequence, color: str | None = None, anno_df: DataFrame | None = None, text_col: str | None = None, index_col: str | None = None, anno_fontsize: int = 12, anno_fontfamily: int = 'Arial', anno_fontstyle: int = 'italic', ax=None, fp=None, **plkwds)

Plot the UMAP embeddings and annotate the names of the given points

Parameters:

  • adt –

  • text_ids – ids of the points to be annotated, corresponding to anno_df.index or anno_df[index_col] (if index_col is given)

  • color – a column name in adt.obs

  • anno_df – use adt.obs as the default annotations.

  • text_col – used as the annotation texts. if specifies, should be a column name in anno_df.

  • index_col – used for index the points, corresponding to text_ids if specifies, should be a column name in anno_df.

  • anno_fontsize – the fontsize of the annotations

  • ax – the plot ax

  • fp – file path for saving the plot.

  • plkwds – other key-word-args for sc.pl.umap

Return type:

ax