grassp.pl.bait_volcano_plots#
- bait_volcano_plots(data, baits=None, sig_cutoff=0.05, lfc_cutoff=2, n_cols=3, base_figsize=5, annotate_top_n=10, color_by=None, highlight=None, title=None, show=False)[source]#
Create volcano plots for bait enrichment analysis.
- Parameters:
- data
AnnData Annotated data matrix with proteins as observations (rows) and baits as variables (columns). Must contain a ‘pvals’ layer with p-values.
- baits
Optional[List[str]] (default:None) List of bait names to plot. If None, plot all baits in data.var_names.
- sig_cutoff
float(default:0.05) P-value significance cutoff for highlighting enriched proteins.
- lfc_cutoff
float(default:2) Log fold change cutoff for highlighting enriched proteins.
- n_cols
int(default:3) Number of columns in the plot grid.
- base_figsize
float(default:5) Base figure size for each subplot.
- annotate_top_n
int(default:10) Number of top proteins to annotate with text labels.
- color_by
Optional[str] (default:None) Column in data.obs to color points by.
- highlight
Optional[List[str]] (default:None) List of protein names to highlight in blue.
- title
Optional[str] (default:None) Title for the overall figure.
- show
bool(default:False) Whether to display the plot.
- data
- Return type:
None|Axes- Returns:
None or matplotlib.axes.Axes If show=True, returns None. Otherwise returns the matplotlib axes.