omicverse.pl.rank_genes_groups_dotplot

omicverse.pl.rank_genes_groups_dotplot(adata, plot_type='dotplot', *, groups=None, n_genes=None, groupby=None, values_to_plot=None, var_names=None, min_logfoldchange=None, key=None, show=None, save=None, return_fig=False, gene_symbols=None, **kwds)[source]

Create a dot plot from rank_genes_groups results.

Parameters:

  • adata (AnnData) – AnnData Annotated data matrix.

  • plot_type (str (default: 'dotplot')) – str Currently only ‘dotplot’ is supported.

  • groups (Union[str, Sequence[str], None] (default: None)) – str or list of str, optional Groups to include in the plot.

  • n_genes (Optional[int] (default: None)) – int, optional Number of genes to include in the plot.

  • groupby (Optional[str] (default: None)) – str, optional Key in adata.obs to group by.

  • values_to_plot (Optional[str] (default: None)) – str, optional Key in rank_genes_groups results to plot (e.g. ‘logfoldchanges’, ‘scores’).

  • var_names (Union[Sequence[str], Mapping[str, Sequence[str]], None] (default: None)) – str or list of str or dict, optional Variables to include in the plot. Can be: - A list of gene names: [‘gene1’, ‘gene2’, …] - A dictionary mapping group names to gene lists: {‘group1’: [‘gene1’, ‘gene2’], ‘group2’: [‘gene3’, ‘gene4’]} When a dictionary is provided, genes will be grouped and labeled accordingly in the plot.

  • min_logfoldchange (Optional[float] (default: None)) – float, optional Minimum log fold change to include in the plot.

  • key (Optional[str] (default: None)) – str, optional Key in adata.uns to use for rank_genes_groups results.

  • show (Optional[bool] (default: None)) – bool, optional Whether to show the plot.

  • save (Optional[bool] (default: None)) – bool, optional Whether to save the plot.

  • return_fig (bool (default: False)) – bool Whether to return the figure object.

  • gene_symbols (Optional[str] (default: None)) – str, optional Key for gene symbols in adata.var.

  • **kwds (Any) – dict Additional keyword arguments to pass to dotplot.

Return type:

Union[Dict, Any, None]

Returns:

If return_fig is True, returns the figure object. If show is False, returns axes dictionary.

Examples

>>> # Basic usage with top genes
>>> ov.pl.rank_genes_groups_dotplot(adata, n_genes=5)

>>> # Using logfoldchanges for coloring
>>> ov.pl.rank_genes_groups_dotplot(adata, n_genes=5, values_to_plot='logfoldchanges')

>>> # Grouping genes manually
>>> gene_groups = {
...     'Group1': ['gene1', 'gene2'],
...     'Group2': ['gene3', 'gene4']
... }
>>> ov.pl.rank_genes_groups_dotplot(adata, var_names=gene_groups)