ligerToSeurat was creating DimReduc objects using new instead of CreateDimReducObject; this caused issues where the DimReduc object was incomplete due to lack of embedding names and empty slots (see satijalab/seurat#3574).
This PR uses Seurat::CreateDimReduc object (called using the :: construct to avoid importing and depending on Seurat) to create dimensional reduction objects to ensure the DimReduc objects are complete. In addition, it uses [[<- to add the dimensional reduction information to ensure that all DimReducs go through proper validation.
ligerToSeuratwas creatingDimReducobjects usingnewinstead ofCreateDimReducObject; this caused issues where theDimReducobject was incomplete due to lack of embedding names and empty slots (see satijalab/seurat#3574).This PR uses
Seurat::CreateDimReducobject (called using the::construct to avoid importing and depending on Seurat) to create dimensional reduction objects to ensure theDimReducobjects are complete. In addition, it uses[[<-to add the dimensional reduction information to ensure that allDimReducsgo through proper validation.