cellrank.tl.kernels.PalantirKernel¶

class
cellrank.tl.kernels.
PalantirKernel
(adata, backward=False, time_key='dpt_pseudotime', compute_cond_num=False, check_connectivity=False)[source]¶ Kernel which computes transition probabilities in a similar way to Palantir, see [Setty19].
Palantir computes a KNN graph in gene expression space and a pseudotime, which it then uses to direct the edges of the KNN graph, such that they are more likely to point into the direction of increasing pseudotime. To avoid disconnecting the graph, it does not remove all edges that point into the direction of decreasing pseudotime but keeps the ones that point to nodes inside a close radius. This radius is chosen according to the local density.
The implementation presented here won’t exactly reproduce the original Palantir algorithm (see below) but the results are qualitatively very similar.
Optionally, we apply a density correction as described in [Coifman05], where we use the implementation of [Haghverdi16].
 Parameters
Attributes
Annotated data object.
Direction of the process.
Condition number of the transition matrix.
Get the kernels of the kernel expression, except for constants.
Parameters which are used to compute the transition matrix.
Pseudotemporal ordering of cells.
Return rownormalized transition matrix.
Methods
compute_transition_matrix
([k, density_normalize])Compute transition matrix based on KNN graph and pseudotemporal ordering.
copy
()Return a copy of self.
read
(fname)Deserialize self from a file.
write
(fname[, ext])Serialize self to a file.
write_to_adata
([key])Write the transition matrix and parameters used for computation to the underlying
adata
object.