scvelo.pl.velocity

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=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.

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.