bioalpha.singlecell.plotting.rank_genes_groups_volcano

bioalpha.singlecell.plotting.rank_genes_groups_volcano(adata: AnnData, group: str | None = None, n_genes: int | None = None, gene_symbols: str | None = None, min_logfoldchange: float | None = None, key: str = 'rank_genes_groups', min_fdr: int = 0.05, show: bool | None = None, save: Path | None = None, **kwds)

Plot ranking of genes using volcano plot.

Parameters:

  • adata (AnnData) – The annotated data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to genes.

  • group (Optional[str]) – The groups for which to show the gene ranking. If group is None, set it to adata.uns[key]['names'].

  • n_genes (Optional[int], default = None) – Number of genes to show.

  • gene_symbols (Optional[str], default = None) – Column name in adata.var that store the symbols of gene.

  • min_logfoldchange (Optional[float], default = None) – Value to filter genes in groups if their logfoldchange is less than the min_logfoldchange.

  • key (str, default = "rank_genes_groups") – Key used to plot the ranking results that stored in adata.uns.

  • min_fdr (int, default = 0.05) – Value to filter genes in groups if their fdr is less than the min_fdr.

  • show (Optional[bool], default = None) – Show the plot, do not return axis.

  • save (Optional[Path], default = None) – If a path is passed, save the figure as a html, otherwise save file with name "{key}_volcano.html".

  • kwds (dict) – Keyword arguments passed to plotly.express.scatter.