scvelo.pl.velocity¶
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scvelo.pl.velocity(adata, var_names=None, basis=None, vkey='velocity', mode=None, fits=None, layers='all', color=None, color_map=None, colorbar=True, perc=[2, 98], 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.
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: [‘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.
- adata :