AzimuthReference

The Azimuth package provides the function AzimuthReference to generate an Azimuth compatible reference (meeting the specifications above) from an existing Seurat object. An example of its usage is below:

ref <- AzimuthReference(
  object = ref,
  refUMAP = "umap",
  refDR = "pca",
  metadata = c("class_label", "cluster_label", "subclass_label", "cross_species_cluster_label"),
  dims = 1:50,
  k.param = 31
)
saveRDS(ref, file = "ref.Rds")

For more examples, please see the azimuth-references repository.

Saving the annoy index

In addition to the ref.Rds file, Azimuth requires a pre-computed annoy index on the reference data. This can be saved to a file with the SaveAnnoyIndex function.

SaveAnnoyIndex(object = ref["refdr.annoy.neighbors"](/satijalab/azimuth/wiki/"refdr.annoy.neighbors"), file = "idx.annoy")

Validating an Azimuth Reference

The Azimuth package also provides a validation function called ValidateAzimuthReference to check that a given Seurat object meets the specifications outlined above.