multivelovae.differential_dynamics_plot

multivelovae.differential_dynamics_plot(adata, genes, group1=None, group2=None, var='v', signed_velocity=True, color_by=None, color_include=None, t_min=None, t_max=None, key='vae', n_bins=50, n_samples=100, seed=0, kernel='RBF', p_value=True, n_cols=5, figsize=None, plot_equal=True, axis_on=True, frame_on=True, title=True, legend=True)

Plot differential dynamics between two groups of cells.

Args:

adata (anndata.AnnData):

Anndata object with differential dynamics results stored in adata.uns[‘differential_dynamics’].

genes (str, list of str):

List of genes to plot.

group1 (str, optional):

Name of group 1. Defaults to None.

group2 (str, optional):

Name of group 2. Defaults to None.

var (str, optional):

Variable to plot. Defaults to velocity ‘v’.

signed_velocity (bool, optional):

Whether to use original velocity values or absolute values. Defaults to True.

color_by: (str, optional):

Color used for the plots. Defaults to None.

color_include (list, optional):

List of categories such as cell types to include in the plot. Defaults to None.

t_min (float, optional):

Minimum time point to include in the plot. Defaults to None.

t_max (float, optional):

Maximum time point to include in the plot. Defaults to None.

key (str, optional):

Key to find VAE variables. Defaults to vae.

n_bins (int, optional):

Number of bins to divide the time points. Defaults to 50.

n_samples (int, optional):

Number of data points to permute in each bin for each group. Defaults to 100.

seed (int, optional):

Seed for random generator. Defaults to 0.

kernel (str, optional):

Kernel to use for Gaussian Process regression. Defaults to ‘RBF’.

p_value (bool, optional):

Whether to show p-value in the plot. Defaults to True.

n_cols (int, optional):

Number of columns to plot. Defaults to 5.

figsize (tuple, optional):

Total figure size. Defaults to None.

plot_equal (bool, optional):

Whether to plot equal time points. Defaults to True.

axis_on (bool, optional):

Whether to show axis labels. Defaults to True.

frame_on (bool, optional):

Whether to show plot frames. Defaults to True.

title (bool, optional):

Whether to show title. Defaults to True.

legend (bool, optional):

Whether to show legend. Defaults to True.