omicverse.pl.complexheatmap

omicverse.pl.complexheatmap(adata, groupby='', figsize=(6, 10), layer=None, use_raw=False, var_names=None, gene_symbols=None, standard_scale=None, col_color_bars=None, col_color_labels=None, left_color_bars=None, left_color_labels=None, right_color_bars=None, right_color_labels=None, marker_genes_dict=None, index_name='', value_name='', cmap='parula', xlabel=None, ylabel=None, label='', save=False, save_pathway='', legend_gap=7, legend_hpad=0, show=False, left_add_text=False, col_split_gap=1, row_split_gap=1, col_height=4, left_height=4, right_height=4, col_cluster=False, row_cluster=False, row_split=None, col_split=None, legend=True, plot_legend=True, right_fontsize=12)[source]

Generate a complex annotated heatmap using PyComplexHeatmap.

Parameters:

  • adata – Annotated data object containing expression data

  • groupby (default: '') – Grouping variable for cell categorization

  • figsize (default: (6, 10)) – Figure dimensions as (width, height)

  • layer (str (default: None)) – Data layer to use for expression values

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

  • var_names (default: None) – List of genes to include in heatmap

  • gene_symbols (default: None) – Gene symbol column name

  • standard_scale (str (default: None)) – Standardization method - ‘obs’, ‘var’, or None

  • col_color_bars (dict (default: None)) – Color mapping dictionary for column annotations

  • col_color_labels (dict (default: None)) – Color mapping for column labels

  • left_color_bars (dict (default: None)) – Color mapping for left annotations

  • left_color_labels (dict (default: None)) – Color mapping for left labels

  • right_color_bars (dict (default: None)) – Color mapping for right annotations

  • right_color_labels (dict (default: None)) – Color mapping for right labels

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

  • index_name (str (default: '')) – Name for index column in melted data

  • value_name (str (default: '')) – Name for value column in melted data

  • cmap (str (default: 'parula')) – Colormap for heatmap values

  • xlabel (str (default: None)) – X-axis label

  • ylabel (str (default: None)) – Y-axis label

  • label (str (default: '')) – Plot label

  • save (bool (default: False)) – Whether to save the plot

  • save_pathway (str (default: '')) – File path for saving

  • legend_gap (int (default: 7)) – Gap between legend items

  • legend_hpad (int (default: 0)) – Horizontal padding for legend

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

  • left_add_text (bool (default: False)) – Whether to add text to left annotations

  • col_split_gap (int (default: 1)) – Gap between column splits

  • row_split_gap (int (default: 1)) – Gap between row splits

  • col_height (int (default: 4)) – Height of column annotations

  • left_height (int (default: 4)) – Height of left annotations

  • right_height (int (default: 4)) – Height of right annotations

  • col_cluster (bool (default: False)) – Whether to cluster columns

  • row_cluster (bool (default: False)) – Whether to cluster rows

  • row_split (default: None) – Row splitting variable

  • col_split (default: None) – Column splitting variable

  • legend (bool (default: True)) – Whether to show legend

  • plot_legend (bool (default: True)) – Whether to plot legend

  • right_fontsize (int (default: 12)) – Font size for right annotations

Returns:

PyComplexHeatmap ClusterMapPlotter object

Return type:

cm