SaveH5Seurat output lacks UMAP slot

[rhodesch]

My object has a UMAP slot named something other that the default "umap". Saving the object with SaveH5Seurat, the UMAP is lost. I have used the same SeuratDisk installation to save a reference Seurat object. In that case, the UMAP slot (named "umap") is correctly added to the h5seurat file.

Save Seurat object in RDS and h5Seurat formats:

saveRDS(object = query, file = "query.rds")
SeuratDisk::SaveH5Seurat(object = query, file = "query.h5seurat", overwrite = TRUE)

Inspect files in new R session:

rds = readRDS("query.rds")

h5 = LoadH5Seurat("query.h5seurat")
Validating h5Seurat file
Warning: Cannot find assay RNA in the H5Seurat file
Initializing Gene.Expression with data
Adding counts for Gene.Expression
Adding miscellaneous information for Gene.Expression
Initializing prediction.score.class with data
Adding miscellaneous information for prediction.score.class
Initializing prediction.score.cluster with data
Adding miscellaneous information for prediction.score.cluster
Initializing prediction.score.cross_species_cluster with data
Adding miscellaneous information for prediction.score.cross_species_cluster
Initializing prediction.score.subclass with data
Adding miscellaneous information for prediction.score.subclass
Initializing refAssay with data
Adding counts for refAssay
Adding scale.data for refAssay
Adding variable feature information for refAssay
Adding miscellaneous information for refAssay
Adding reduction integrated_dr
Adding cell embeddings for integrated_dr
Adding miscellaneous information for integrated_dr
Adding neighbors query_ref.nn
Adding command information
Adding cell-level metadata
Adding miscellaneous information
Adding tool-specific results

> rds
An object of class Seurat 
73399 features across 105469 samples within 6 assays 
Active assay: refAssay (36601 features, 2248 variable features)
 5 other assays present: Gene.Expression, prediction.score.class, prediction.score.subclass, prediction.score.cluster, prediction.score.cross_species_cluster
 2 dimensional reductions calculated: integrated_dr, proj.umap

> h5
An object of class Seurat 
73399 features across 105469 samples within 6 assays 
Active assay: refAssay (36601 features, 2248 variable features)
 5 other assays present: Gene.Expression, prediction.score.class, prediction.score.cluster, prediction.score.cross_species_cluster, prediction.score.subclass
 1 dimensional reduction calculated: integrated_dr