omicverse.pl.group_heatmap

omicverse.pl.group_heatmap(adata, var_names, groupby, *, figsize=(6, 10), layer=None, use_raw=False, gene_symbols=None, standard_scale=None, cmap='RdBu_r', row_cluster=False, col_cluster=False, row_split=None, col_split=None, left_color_bars=None, left_color_labels=None, right_color_bars=None, right_color_labels=None, col_color_bars=None, legend=True, legend_style='tight', border=False, label='Mean expression', save=False, save_pathway='', show=False)[source]

Plot grouped mean expression as a Marsilea heatmap.

Parameters:

  • adata (AnnData) – Annotated data matrix containing the expression values.

  • var_names – Features to plot. Accepts a list of genes, a single gene name, or a mapping of group label to gene list.

  • groupby (str) – Key in adata.obs used to aggregate cells into groups.

  • figsize (tuple (default: (6, 10))) – Figure size (width, height) in inches.

  • layer (str (default: None)) – Expression source selection passed through to obs_df.

  • use_raw (bool (default: False)) – Expression source selection passed through to obs_df.

  • gene_symbols (str (default: None)) – Expression source selection passed through to obs_df.

  • standard_scale (str (default: None)) – Optional scaling mode. Supported values are 'obs', 'var', or None.

  • cmap (str (default: 'RdBu_r')) – Colormap used for the heatmap body.

  • row_cluster (bool (default: False)) – Whether to add hierarchical dendrograms for rows or columns.

  • col_cluster (bool (default: False)) – Whether to add hierarchical dendrograms for rows or columns.

  • row_split (default: None) – Optional explicit ordering of row or column groups.

  • col_split (default: None) – Optional explicit ordering of row or column groups.

  • left_color_bars (dict (default: None)) – Optional annotation palettes or labels for row-side annotations.

  • left_color_labels (dict (default: None)) – Optional annotation palettes or labels for row-side annotations.

  • right_color_bars (dict (default: None)) – Optional annotation palettes or labels for row-side annotations.

  • right_color_labels (dict (default: None)) – Optional annotation palettes or labels for row-side annotations.

  • col_color_bars (dict (default: None)) – Optional palette for grouped column annotations.

  • legend (bool (default: True)) – Legend visibility and layout strategy.

  • legend_style (str (default: 'tight')) – Legend visibility and layout strategy.

  • border (bool (default: False)) – Whether to draw a visible border around heatmap axes after rendering.

  • label (str (default: 'Mean expression')) – Label used for the heatmap value legend.

  • 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