- dynamo.tl.velocity_N(adata, group=None, recalculate_pca=True, recalculate_umap=True, del_2nd_moments=None)
use new RNA based pca, umap, for velocity calculation and projection for kinetics or one-shot experiment.
Note that currently velocity_N function only considers labeling data and removes splicing data if they exist.
AnnData) – AnnData object that stores data for the the kinetics or one-shot experiment, must include X_new, X_total layers.
group (str or None (default: None)) – The cell group that will be used to calculate velocity in each separate group. This is useful if your data comes from different labeling condition, etc.
recalculate_pca (bool (default: True)) – Whether to recalculate pca with the new RNA data. If setting to be False, you need to make sure the pca is already generated via new RNA.
recalculate_umap (bool (default: True)) – Whether to recalculate umap with the new RNA data. If setting to be False, you need to make sure the umap is already generated via new RNA.
del_2nd_moments (None or bool) – Whether to remove second moments or covariances. Default it is None rgument used for dynamics function.
Nothing but the adata object is updated with the low dimensional (umap or pca) velocity projections with the
new RNA or pca based RNA velocities.