omicverse.pl.cell_cor_heatmap

omicverse.pl.cell_cor_heatmap(adata, group_by, *, ref_adata=None, ref_group_by=None, features=None, n_features=2000, method='pearson', layer=None, use_raw=False, standard_scale='var', cmap='RdBu_r', figsize=(6, 6), show_values=True, value_fmt='.2f', row_cluster=True, col_cluster=True, vmin=None, vmax=None, legend=True, legend_style='tight', border=False, save=False, save_pathway='', show=False)[source]

Compute pairwise correlation/similarity between cell groups and plot as heatmap.

Mirrors scop::CellCorHeatmap — computes group-level mean expression and plots the resulting similarity matrix.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • group_by (str) – Key in adata.obs for grouping cells (e.g. 'cell_type').

  • ref_adata (AnnData (default: None)) – Optional second AnnData for cross-dataset comparison. If None, the query adata is used as both query and reference.

  • ref_group_by (str (default: None)) – Grouping key in ref_adata. Defaults to group_by.

  • features (default: None) – Specific features to use. If None, highly-variable genes are used.

  • n_features (int (default: 2000)) – Number of top variable features to select when features is None.

  • method (str (default: 'pearson')) – Similarity metric: 'pearson', 'spearman', or 'cosine'.

  • layer (str (default: None)) – Which expression slot to read.

  • use_raw (bool (default: False)) – Which expression slot to read.

  • standard_scale (str (default: 'var')) – 'var' (per-gene) or 'obs' (per-cell) z-scoring.

  • cmap (str (default: 'RdBu_r')) – Colour map for the heatmap.

  • figsize (tuple (default: (6, 6))) – Figure size (width, height) in inches.

  • show_values (bool (default: True)) – Whether to print correlation values inside cells.

  • value_fmt (str (default: '.2f')) – Format string for printed values (e.g. '.2f').

  • row_cluster (bool (default: True)) – Whether to hierarchically cluster rows / columns.

  • col_cluster (bool (default: True)) – Whether to hierarchically cluster rows / columns.

  • vmin (float (default: None)) – Colour limits.

  • vmax (float (default: None)) – Colour limits.

  • legend (bool (default: True)) – Show colour bar.

  • save (bool | str (default: False)) – Output controls. save may be True/False or a concrete path.

  • save_pathway (str (default: '')) – Output controls. save may be True/False or a concrete path.

  • show (bool (default: False)) – Output controls. save may be True/False or a concrete path.

Returns:

Returns the Marsilea plotter by default, or the rendered figure when rendering is triggered for saving/showing/tight legends.

Return type:

marsilea.Heatmap or matplotlib.figure.Figure