omicverse.pl.marker_heatmap

omicverse.pl.marker_heatmap(adata, marker_genes_dict=None, groupby=None, color_map='RdBu_r', use_raw=True, standard_scale='var', expression_cutoff=0.0, bbox_to_anchor=(5, -0.5), figsize=(8, 4), spines=False, fontsize=12, show_rownames=True, show_colnames=True, save_path=None, ax=None)[source]

Create a dot plot heatmap showing marker gene expression using PyComplexHeatmap.

Parameters:

  • adata (AnnData) – Annotated data object with expression data

  • marker_genes_dict (dict (default: None)) – Dictionary mapping cell types to marker genes

  • groupby (str (default: None)) – Column name for cell type grouping

  • color_map (str (default: 'RdBu_r')) – Colormap for expression values

  • use_raw (bool (default: True)) – Whether to use raw expression data

  • standard_scale (str (default: 'var')) – Expression standardization method

  • expression_cutoff (float (default: 0.0)) – Minimum expression threshold

  • bbox_to_anchor (tuple (default: (5, -0.5))) – Legend position

  • figsize (tuple (default: (8, 4))) – Figure dimensions

  • spines (bool (default: False)) – Whether to show plot spines

  • fontsize (int (default: 12)) – Font size for labels

  • show_rownames (bool (default: True)) – Whether to display row names

  • show_colnames (bool (default: True)) – Whether to display column names

  • save_path (str (default: None)) – File path for saving plot

  • ax (default: None) – Existing matplotlib axes object

Returns:

matplotlib.figure.Figure object ax: matplotlib.axes.Axes object

Return type:

fig