spcoral.plot.show_cross_anchor_heatmap

spcoral.plot.show_cross_anchor_heatmap#

spcoral.plot.show_cross_anchor_heatmap(adata_omics1, adata_omics2, registering_parameters, celltype_label=None, heatmap_cmap='viridis', bar_palette=None, figsize=None, dpi=None, title=None, norm_axis=None, show=True, save=None, omics1_bar_kwargs=None, omics2_bar_kwargs=None, **kwargs)#

Visualize the cross-modality anchor correspondence as a heatmap with optional cell-type side bars.

Parameters:

  • adata_omics1 (anndata.AnnData) – First (source) omics AnnData object containing anchor spots.

  • adata_omics2 (anndata.AnnData) – Second (target) omics AnnData object containing corresponding anchor spots.

  • registering_parameters (dict) – Dictionary or list from registration output, expected to contain: - Index 1: array of anchor indices in adata_omics1 - Index 2: array of corresponding anchor indices in adata_omics2 (typically registering_parameters = [T, omics1_index, omics2_index])

  • celltype_label (str, optional) – Column name in .obs containing cell-type or cluster annotations. If None, raw counts without labels are used (indices as categories).

  • heatmap_cmap (str, optional (default: 'viridis')) – Colormap for the central correspondence heatmap.

  • bar_palette (list or dict, optional) – Custom color palette for cell-type side bars. If list, colors are assigned sequentially; if dict, maps cell types to colors. If None, automatically generated using _get_color.

  • figsize (tuple of (float, float), optional) – Figure size passed to matplotlib.

  • dpi (float, optional) – Figure resolution.

  • title (str, optional) – Figure title.

  • norm_axis ({0, 1}, optional) – Axis along which to normalize heatmap values to proportions: - 0: row-wise (proportion of omics2 types per omics1 type) - 1: column-wise - None: raw counts

  • show (bool, optional (default: True)) – Whether to display the figure immediately.

  • save (str or PathLike, optional) – Path to save the figure. If provided, figure is saved (format inferred from extension).

  • omics1_bar_kwargs (dict, optional) – Additional keyword arguments passed to the horizontal/vertical side bar plots.

  • omics2_bar_kwargs (dict, optional) – Additional keyword arguments passed to the horizontal/vertical side bar plots.

  • **kwargs (Any) – Additional arguments passed to the underlying _heatmap_with_dendrogram_and_bar function.

Returns:

Figure and axes if show=False; otherwise None (figure is displayed).

Return type:

tuple of (matplotlib.figure.Figure, axes) or None

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