CellRank dev (2022-04-28)

Features

• Update CytoTRACE calculation to check inf vals #761

• Refactor cellrank.tl.kernels.TransportMapKernel for easier definition of extensions. #764

• Allow plotting negatively correlated genes in cellrank.pl.lineage_drivers(). #779

• Refactor kernel module. These changes include: - allow kernel elementwise multiplication - decouple CytoTRACE computation from kernel initialization, see cellrank.tl.kernels.CytoTRACEKernel.compute_cytottrace() - change argument mode to model in cellrank.tl.kernels.VelocityKernel - change argument scheme to similarity in cellrank.tl.kernels.VelocityKernel - remove 'sampling' option in cellrank.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 - improve cellrank.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 in cellrank.tl.kernels.TransportMapKernel - fix automatic threshold removing 1 row in cellrank.tl.kernels.TransportMapKernel #791

• Allow local block-diagonal connectivities in cellrank.tl.kernels.TransportMapKernel. Rename last_time_point argument to self_transitions and add conn_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. #748

• Fix when associating term/macro states assignment when reference is not categorical string. #750

• Fix color creating in cellrank.tl.kernels.ExperimentalTimeKernel. #784

• Fix 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. #835

• Do not save enums in anndata.AnnData. #842

• Fix cellrank.tl.Lineage subsetting (non-existent overlapping keys) and refactor the implementation. #861

Miscellaneous

• Ignore pygam deprecation warnings. #798

• Fix PETSc/SLEPc in CI for Linux. For now, macOS PETSc/SLEPc remains disabled. #850