grassp.pl.highly_variable_proteins

highly_variable_proteins(adata_or_result, *, highly_variable_proteins=True, show=None, save=None, log=False)

Plot dispersions versus means for highly variable proteins.

Parameters:

adata_or_result AnnData | DataFrame | recarray

Annotated data matrix or DataFrame/recarray containing results from highly_variable_proteins computation.

highly_variable_proteins bool (default: True)

Whether to plot highly variable proteins or all proteins. Default: True.

show Optional[bool] (default: None)

Show the plot. If None, use scanpy’s plotting settings.

save Union[bool, str, None] (default: None)

If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {‘.pdf’, ‘.png’, ‘.svg’}.

log bool (default: False)

Plot on log scale. Default: False.

Return type:

None | Axes

Returns:

matplotlib.pyplot.Axes or None If show=False, returns matplotlib axes object. Otherwise returns None and shows or saves the plot.

Notes

This is a modified version of scanpy’s highly_variable_genes plot adapted for proteomics data. It shows the relationship between mean protein intensity and dispersion/variance, highlighting highly variable proteins.