multivelovae.dynamic_plot

multivelovae.dynamic_plot(adata, adata_atac, genes, key='vae', by='expression', modalities=None, modalities_pred=None, color_by=None, axis_on=True, frame_on=True, show_pred=True, show_pred_only=False, batch_correction=False, downsample=1, figsize=None, pointsize=2, cmap='coolwarm')

Gene dynamics plot.

This function plots accessibility, expression, or velocity by time.

Args:

adata anndata.AnnData:

Anndata result after VAE inference.

adata_atac anndata.AnnData:

ATAC Anndata object.

genes [str, list of str]:

List of genes to plot.

key (str, optional):

Key to find VAE variables. Defaults to vae.

by (str, optional):

Plot accessibilities and expressions if expression. Plot velocities if velocity. Defaults to expression.

modalities (list, optional):

List of modalities in adata.layers to plot. Defaults to None.

modalities_pred (list, optional):

List of predicted modalities in adata.layers to plot. Defaults to None.

color_by: (str, optional):

Color used for the plots. Defaults to None.

axis_on (bool):

Whether to show axis labels. Defaults to True.

frame_on (bool):

Whether to show plot frames. Defaults to True.

show_pred (bool):

Whether to show prediction. Defaults to True.

show_pred_only (bool):

Whether to show prediction only. Defaults to False.

batch_correction (bool):

Whether the output was generated with batch correction. Defaults to False.

downsample (int):

How much to downsample the cells. The remaining number will be 1/downsample of original. Defaults to 1.

figsize (tuple):

Total figure size. Defaults to None.

pointsize (float):

Point size for scatter plots. Defaults to 2.

cmap: (str)

Color map for continuous color key. Defaults to ‘coolwarm’.