scvelo.pl.velocity_embedding_grid

scvelo.pl.velocity_embedding_grid(adata, basis=None, vkey='velocity', density=None, smooth=None, min_mass=None, arrow_size=None, arrow_length=None, arrow_color=None, scale=None, autoscale=True, n_neighbors=None, X=None, V=None, X_grid=None, V_grid=None, principal_curve=False, color=None, use_raw=None, layer=None, color_map=None, colorbar=True, palette=None, size=None, alpha=0.2, perc=None, sort_order=True, groups=None, components=None, projection='2d', legend_loc='none', legend_fontsize=None, legend_fontweight=None, right_margin=None, left_margin=None, xlabel=None, ylabel=None, title=None, fontsize=None, figsize=None, dpi=None, frameon=None, show=True, save=None, ax=None, ncols=None, **kwargs)

Scatter plot of velocities on a grid.

Parameters:
adata : AnnData

Annotated data matrix.

x : str, np.ndarray or None (default: None)

x coordinate

y : str, np.ndarray or None (default: None)

y coordinate

vkey : str or None (default: None)

Key for annotations of observations/cells or variables/genes.

density : float (default: 1)

Amount of velocities to show - 0 none to 1 all

arrow_size : float or 3-tuple for headlength, headwidth and 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 (default: 0.5)

Minimum threshold for mass to be shown.

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

basis : str (default=’umap’)

Key for embedding.

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

Key for annotations of observations/cells or variables/genes

use_raw : bool (default: None)

Use raw attribute of adata if present.

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

Specify the layer for color.

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

String denoting matplotlib color map.

colorbar : bool (default: False)

Whether to show colorbar.

palette : list of str (default: None)

Colors to use for plotting groups (categorical annotation).

size : float (default: 5)

Point size.

alpha : float (default: 1)

Set blending - 0 transparent to 1 opaque.

linewidth : float (default: 1)

Scaling factor for the width of occurring lines.

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

Specify percentile for continuous coloring.

sort_order : bool (default: True)

For continuous annotations used as color parameter, plot data points with higher values on top of others.

groups : str (default: all groups)

Restrict to a few categories in categorical observation annotation.

components : str or list of str (default: ‘1,2’)

For instance, [‘1,2’, ‘2,3’].

projection : {'2d', '3d'} (default: '2d')

Projection of plot.

legend_loc : str (default: 'none')

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

legend_fontsize : int (default: None)

Legend font size.

legend_fontweight : {‘normal’, ‘bold’, …} (default: None)

Legend font weight. Defaults to ‘bold’ if legend_loc = ‘on data’, otherwise to ‘normal’. Available are [‘light’, ‘normal’, ‘medium’, ‘semibold’, ‘bold’, ‘heavy’, ‘black’].

right_margin : float or list of float (default: None)

Adjust the width of the space right of each plotting panel.

left_margin : float or list of float (default: None)

Adjust the width of the space left of each plotting panel.

xlabel : str (default: None)

Label of x-axis.

ylabel : str (default: None)

Label of y-axis.

title : str (default: None)

Provide title for panels either as, e.g. [“title1”, “title2”, …].

fontsize : float (default: None)

Label font size.

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

Figure size.

dpi : int (default: 80)

Figure dpi.

frameon : bool (default: True)

Draw a frame around the scatter plot.

ncols : int (default: None)

Number of panels per row.

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.

Returns:

matplotlib.Axis if show==False