v1.0.4

[dbdimitrov]

1.0.4 (02.01.2024)

• Moved the Global score summaries of SpatialBivariate from .uns to .var

• df_to_lr will now also return the expression and proportion of expression for the interactions

• li.multi.nfm will now also accept a DataFrame as input

• Filtered putative interactions in the Consensus resource, coming from CellTalkDB.

• Changed filter_lambda parameter to filter_fun for consistency and now any function can be passed to be applied as a row-wise filter.

• Global results of SpatialBivariate will now be saved to .var

• LIANA's spatial methods will now work with non-aligned AnnData objects, i.e. when observations across modalities are not aligned.
  = Added li.ut.interpolate_adata utility function to interpolate the data to a common space.
  = MISTy will also work with directly non-aligned data with spatial connectivities from one modality to the other being passed via obsm rather than obsp. Making use of li.ut.spatial_neighbors by passing reference coordinates.

• Fixed a bug where li.ut.obsm_to_adata would assign var as a method rather than DataFrame

• Fixed a bug where p-values for Global Moran's were not calculated correctly.

• Enabled cell_pairs of interest to be passed to single-cell methods.

• Enabled Parallelization of Permutation-based methods.

• Local categories will now be only calculated for positive interactions (not non-ambigous as before).

• Names of source and target can now be passed to li.pl.tileplot.