Seurat v5 not compatible with Azimuth

[chunjie-sam-liu]

I tried to run the command below and get the error becuase of compatibility with Seurat v5

Azimuth::RunAzimuth(
  query = "PBMC_10K_output/filtered_feature_bc_matrix.h5",
  reference = "pbmcref"
)

Error in validObject(object = object) : 
  invalid class “Assay5” object: Layers must be two-dimensional objects
Calls: <Anonymous> ... .CreateStdAssay.list -> LayerData<- -> LayerData<-.Assay5 -> validObject

The error was caused by the SeuratObject:::CreateSeuratObject.default when Azimuth::LoadReference to load the reference cell map.

azimuth/R/azimuth.R

Line 52 in 243ee5d

reference <- LoadReference(reference)$map

For the Seurat version less than v5, it is ok but if the Seurat greater than v5, it will result in invalid class “Assay5” object: Layers must be two-dimensional objects.