omicverse.pl.feature_heatmap

omicverse.pl.feature_heatmap(adata, var_names, *, groupby=None, cell_orderby=None, max_cells=100, figsize=(8, 4), layer=None, use_raw=False, gene_symbols=None, standard_scale='var', cmap='RdBu_r', legend=True, legend_style='tight', border=False, show_row_names=True, show_column_names=False, save=False, save_pathway='', show=False)[source]

Plot cell-level feature expression ordered by groups or metadata.

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 (default: None)) – Optional categorical key in adata.obs used to color and group columns by cell identity.

  • cell_orderby (str (default: None)) – Optional continuous or categorical key in adata.obs used to order cells before plotting.

  • max_cells (int (default: 100)) – Maximum number of cells retained per group when groupby is set.

  • figsize (tuple (default: (8, 4))) – 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: 'var')) – Optional scaling mode. Supported values are 'obs', 'var', 'group', or None.

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

  • 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.

  • show_row_names (bool (default: True)) – Whether to display feature labels on rows or cell labels on columns.

  • show_column_names (bool (default: False)) – Whether to display feature labels on rows or cell labels on columns.

  • 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