evolocity.pl.velocity_contour¶

evolocity.pl.velocity_contour(adata, ptkey='pseudotime', rank_transform=True, use_ends=False, fill=True, levels=10, basis=None, vkey='velocity', density=None, smooth=None, pt_smooth=None, min_mass=None, arrow_size=None, arrow_length=None, arrow_color=None, scale=None, autoscale=True, n_neighbors=None, recompute=None, X=None, V=None, X_grid=None, V_grid=None, PF_grid=None, color=None, layer=None, color_map=None, colorbar=True, palette=None, size=None, alpha=0.5, offset=1, vmin=None, vmax=None, perc=None, sort_order=True, groups=None, components=None, projection='2d', legend_loc='none', legend_fontsize=None, legend_fontweight=None, xlabel=None, ylabel=None, title=None, fontsize=None, figsize=None, dpi=None, frameon=None, show=None, save=None, ax=None, ncols=None, **kwargs)¶

Contour plot of pseudotime with velocity grid.

Parameters

adata : AnnData: Annotated data matrix.
ptkey : str (default: pseudotime): Name of pseudotime values.
rank_transform : bool (default: True): Perform final rank transformation.
use_ends : bool (default: False): Use end terminal nodes in pseudotime computation.
levels : int (default: 10): Number of contour levels.
pt_smooth : float (default: None): Pseudotime two-dimensional smoothing.
density : float (default: 1): Amount of velocities to show - 0 none to 1 all
arrow_size : float or triple headlength, headwidth, headaxislength (default: 1): Size of arrows.
arrow_length : float (default: 1): Length of arrows.
scale : float (default: 1): Length of velocities in the embedding.
min_mass : float or None (default: None): Minimum threshold for mass to be shown. It can range between 0 (all velocities) and 100 (large velocities).
smooth : float (default: 0.5): Multiplication factor for scale in Gaussian kernel around grid point.
n_neighbors : int (default: None): Number of neighbors to consider around grid point.
X : np.ndarray (default: None): embedding grid point coordinates
V : np.ndarray (default: None): embedding grid velocity coordinates
{scatter}

Returns

matplotlib.Axis if show==False