, var_names=None, basis=None, vkey='velocity', mode=None, fits=None, layers='all', color=None, color_map=None, colorbar=True, perc=None, alpha=0.5, size=None, groupby=None, groups=None, legend_loc='none', legend_fontsize=8, use_raw=False, fontsize=None, figsize=None, dpi=None, show=None, 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.

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: [‘velocity’, ‘dynamics’])

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 or tuple (default: [‘RdYlGn’, ‘gnuplot_r’])

String denoting matplotlib color map. If tuple is given, first and latter color map correspond to velocity and expression, respectively.

perc: tuple, e.g. [2,98] (default: [2,98])

Specify percentile for continuous coloring.

groups: str, list (default: None)

Subset of groups, e.g. [‘g1’, ‘g2’], to which the plot shall be restricted.

groupby: str, list or np.ndarray (default: None)

Key of observations grouping to consider.

legend_loc: str (default: ‘none’)

Location of legend, either ‘on data’, ‘right margin’ or valid keywords for matplotlib.legend.

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.

ncols: int or None (default: None)

Number of columns to arange multiplots into.