scvelo.pl.velocity

scvelo.pl.velocity(adata, var_names=None, basis=None, groupby=None, groups=None, mode=None, fits='all', layers='all', color=None, color_map='RdBu_r', colorbar=False, perc=[2, 98], use_raw=False, size=None, alpha=0.5, fontsize=None, figsize=None, dpi=None, show=True, save=None, ax=None, ncols=None, **kwargs)

Phase and velocity plot for set of genes.

The phase plot shows spliced against unspliced expressions with steady-state fit. Further the embedding is shown colored by velocity and expression.

Parameters:
adata : AnnData

Annotated data matrix.

var_names : str or list of str (default: None)

Which variables to show.

basis : str (default: ‘umap’)

Key for embedding coordinates.

mode : ‘stochastic’ or None (default: None)

Whether to show show covariability phase portrait.

fits : str or list of str (default: ‘all’)

Which steady-state estimates to show.

layers : str or list of str (default: ‘all’)

Which layers to show.

color : str, list of str or None (default: None)

Key for annotations of observations/cells or variables/genes

color_map : str (default: matplotlib.rcParams[‘image.cmap’])

String denoting matplotlib color map.

perc : tuple, e.g. [2,98] (default: None)

Specify percentile for continuous coloring.

size : float (default: 5)

Point size.

alpha : float (default: 1)

Set blending - 0 transparent to 1 opaque.

fontsize : float (default: None)

Label font size.

figsize : tuple (default: (7,5))

Figure size.

dpi : int (default: 80)

Figure dpi.

show : bool, optional (default: None)

Show the plot, do not return axis.

save : bool or str, optional (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’}.

ax : matplotlib.Axes, optional (default: None)

A matplotlib axes object. Only works if plotting a single component.