Added a check for the subset of cell types in li.multi.dea_to_lr. Related to #92.
Split Local and Global Bivariate metrics. Specifically, I reworked completely the underlying code, though the API should remain relatively unchanged. With the exceptions of: 1) lr_bivar is now removed and bivar has been renamed to bivariate. This allowed me to remove a lot of redundancies between the two functions. 2) nz_threshold has been renamed to nz_prop for consistency with expr_prop in the remainder of the package. Related to #44.
li.mt.bivariate parameter mod_added has been renamed to key_added due to this now refer to both .obsm and .mod - depedening whether an AnnData or MuData object is passed.
Added Global Lee's statistic, along with a note on weighted product that upon z-scaling it is equivalent to Lee's local statistic.
The Global L statistic and Global Moran's R are themselves basically identical. See Eq.22 from Lee and Eq.1 in Supps of SpatialDM.
Changed the li.mt.bivar parameter function_name to local_name for consistency and to avoid ambiguity with the newly-added global_name parameter.
Added bumpversion to manage versioning. Related to #73.
Added max_runs and stable_runs parameters to enable the inference of robust causal networks with CORNETO. Related to #82.
Optimized MISTy such that the matrix multiplication by weights is done only once, rather than for each target. Users can now obtain the weighted matrix via the misty.get_weighted_matrix function.
MISTy models are now passed externally, rather than being hardcoded. This allows for more flexibility in the models used. As an example, I also added a RobustLinearModel from statsmodels. Related to #74.
Removed forced conversion to sparse csr_matrix matrices in MISTy. Related to #57.
1.1.0 (12.04.2024)
Added a check for the subset of cell types in li.multi.dea_to_lr. Related to #92.
Split Local and Global Bivariate metrics. Specifically, I reworked completely the underlying code, though the API should remain relatively unchanged. With the exceptions of: 1)
lr_bivaris now removed andbivarhas been renamed tobivariate. This allowed me to remove a lot of redundancies between the two functions. 2)nz_thresholdhas been renamed tonz_propfor consistency withexpr_propin the remainder of the package. Related to #44.li.mt.bivariateparametermod_addedhas been renamed tokey_addeddue to this now refer to both.obsmand.mod- depedening whether an AnnData or MuData object is passed.Added Global Lee's statistic, along with a note on weighted product that upon z-scaling it is equivalent to Lee's local statistic.
The Global L statistic and Global Moran's R are themselves basically identical. See Eq.22 from Lee and Eq.1 in Supps of SpatialDM.
Changed the
li.mt.bivarparameterfunction_nametolocal_namefor consistency and to avoid ambiguity with the newly-addedglobal_nameparameter.Added
bumpversionto manage versioning. Related to #73.Added
max_runsandstable_runsparameters to enable the inference of robust causal networks with CORNETO. Related to #82.Optimized MISTy such that the matrix multiplication by weights is done only once, rather than for each target. Users can now obtain the weighted matrix via the
misty.get_weighted_matrixfunction.MISTy models are now passed externally, rather than being hardcoded. This allows for more flexibility in the models used. As an example, I also added a RobustLinearModel from statsmodels. Related to #74.
Removed forced conversion to sparse csr_matrix matrices in MISTy. Related to #57.