CellRank 1.5.0 (2021-09-13)#
Features#
Add
threshold
tocellrank.external.kernels.WOTKernel.compute_transition_matrix()
to increase sparsity and speed upcellrank.tl.estimators.GPCCA
. #696Allow using columns from
anndata.AnnData.var
as gene symbols for some plotting functions. #726Completely refactor
cellrank.tl.estimators
. This includes the following changes:define less coupled, more extensible class hierarchy.
follow more closely fit/predict paradigm of
sklearn
, see e.g.cellrank.tl.estimators.GPCCA.fit()
andcellrank.tl.estimators.GPCCA.predict()
.make estimators implicitly maintain a more consistent state.
remove plotting of Schur vectors and eigenvectors in an embedding.
remove cell-cycle warning for terminal states.
remove
is_irreducible
,recurrent_classes
andtransient_classes
properties.remove optional irreducibility check from
cellrank.tl.estimators.GPCCA.compute_absorption_probabilities()
normalize estimator attribute names and key names when writing to
anndata.AnnData
.allow estimators to serialize self from/to
anndata.AnnData
, seecellrank.tl.estimators.BaseEstimator.from_adata()
orcellrank.tl.estimators.BaseEstimator.to_adata()
.allow estimators to be saved to a file without it
anndata.AnnData
.improve docstrings in various places.
write lineage drivers to
anndata.AnnData.varm
instead ofanndata.AnnData.var
.fix various corner cases when solving linear systems (e.g. only 1 variable).
In addition, add
cellrank.tl.Lineage.from_adata()
to allow easy reconstruction of lineage objects. #727
Bugfixes#
Fix
towncrier
release generation CI. #701Update
towncrier
to display development release notes. #709Restricts computation of embedding projection to kNN based kernels. #733
Fix
cellrank.external.kernels.WOTKernel.compute_transition_matrix()
silently ignoring unexpected kwargs. #737Use actual number of nearest neighbors in
cellrank.tl.kernels.PseudotimeKernel
when using hard threshold scheme. #738Fix
cellrank.pl.cluster_lineage()
sometimes reusing the same ax. #742
Deprecations (in next major release)#
Deprecate
cellrank.tl
, including the high level API and renamecellrank.ul.models
tocellrank.models
. #695