CellRank dev (2022-04-28)
Features
Update CytoTRACE calculation to check inf vals #761
Refactor
cellrank.tl.kernels.TransportMapKernel
for easier definition of extensions. #764Allow plotting negatively correlated genes in
cellrank.pl.lineage_drivers()
. #779Refactor kernel module. These changes include: - allow kernel elementwise multiplication - decouple CytoTRACE computation from kernel initialization, see
cellrank.tl.kernels.CytoTRACEKernel.compute_cytottrace()
- change argumentmode
tomodel
incellrank.tl.kernels.VelocityKernel
- change argumentscheme
tosimilarity
incellrank.tl.kernels.VelocityKernel
- remove'sampling'
option incellrank.tl.kernels.VelocityKernel
- distinguish between unidirectional and bidirectional kernels - bidirectional kernel inversion is no longer inplace, returns a new object - add more memory efficient way of copying kernels - improvecellrank.kernels.PrecomputedKernel
- abstract kernel-related plotting functions (projection and random walks) - temporarily remove kernel tricks examples - fix various typos in docstrings - fix corner-case bug when computing absorption probabilities - fix not setting transport maps incellrank.tl.kernels.TransportMapKernel
- fix automatic threshold removing 1 row incellrank.tl.kernels.TransportMapKernel
#791Allow local block-diagonal connectivities in
cellrank.tl.kernels.TransportMapKernel
. Renamelast_time_point
argument toself_transitions
and addconn_weight
.self_transitions
can also be applied to specific diagonal blocks only. #828
Bugfixes
Fix
cellrank.external.kernels.WOTKernel
saving OTModel and being unable to pickle itself. #748Fix when associating term/macro states assignment when reference is not categorical string. #750
Fix color creating in
cellrank.tl.kernels.ExperimentalTimeKernel
. #784Fix all q-values being NaN if 1 p-value was NaN. Also warn and set to NaN instead of raise when correlations are not in
[0, 1]]
interval. #835Do not save enums in
anndata.AnnData
. #842Fix
cellrank.tl.Lineage
subsetting (non-existent overlapping keys) and refactor the implementation. #861