multivelovae.decoupling_plot

multivelovae.decoupling_plot(adata, genes, group1=None, group2=None, absolute=False, show_coupling=True, show_decoupling=True, color_by=None, color_include=None, key='vae', n_bins=50, n_samples=100, seed=0, use_gp=False, kernel='RBF', n_cols=5, figsize=None, axis_on=True, frame_on=True, title=True, legend=True)

Plot decoupling or coupling dynamics between two groups of cells.

Args:

adata (anndata.AnnData):

AnnData object with differential dynamics results.

genes (str or 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.

absolute (bool, optional):

Whether to plot absolute (de)coupling values. Defaults to False.

show_coupling (bool, optional):

Whether to show coupling values in the plot. Defaults to True.

show_decoupling (bool, optional):

Whether to show decoupling values in the plot. Defaults to True.

color_by (str, optional):

Key in adata.obs to color the points by. Defaults to None.

color_include (list, optional):

List of categories to include in the color_by variable. 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.

n_cols (int, optional):

Number of columns to plot. Defaults to 5.

figsize (tuple, optional):

Total figure size. Defaults to None.

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.