Seurat to Loupe

library(Seurat)
## Prep for 10x loupe browser inegration
seurat.object 

### first we need to extract out the seurat cell barcodes and convert them back into Loupe space
### note this is tested on integrated objects in seurat with multi samples
seurat.object$loupe_barcodes <- gsub(names(Idents(seurat.object)),pattern = "-1_",replacement = "-")

## pull the embeddings from UMAP
embeds <- (seurat.object@reductions$umap@cell.embeddings)
rownames(embeds) <- seurat.object$loupe_barcodes

write.csv(file="loupe-files/umap.embeddings.csv",
          embeds,
          row.names = T,col.names = F,quote = F)

## next we want to grab the clustering and save that out 
loupe_clusts <- data.frame(seurat.object$seurat_clusters)
rownames(loupe_clusts) <- seurat.object$loupe_barcodes
write.csv(file="loupe-files/umap.clustering.csv",
          loupe_clusts,
          row.names = T,col.names = F,quote = F)

## barcode to our custom labels
loupe_labels <- data.frame(Idents(seurat.object))
rownames(loupe_labels) <- seurat.object$loupe_barcodes
write.csv(file="loupe-files/umap.cellTypeLabel.csv",
          loupe_labels,
          row.names = T,col.names = F,quote = F)

## lastly sample + cell type
seurat.object$id_type <- paste0(Idents(seurat.object),"-",seurat.object$orig.ident)
loupe_ids <- data.frame(seurat.object$id_type)
rownames(loupe_ids) <- seurat.object$loupe_barcodes