# UPDATE THESE PATHS TO REFLECT WHERE YOU HAVE PUT THE FILES:
path.to.seurat.object <- "Daniocell2023_SeuratV4.rds"
path.to.annotations <- "Daniocell_annotations.csv"

# Load the Daniocell Seurat object and the latest annotations
daniocell <- readRDS(path.to.seurat.object)
daniocell.annot <- read.csv(path.to.annotations)

# To add the latest annotations to the Seurat metadata
rownames(daniocell.annot) <- daniocell.annot$clust
daniocell.annot <- daniocell.annot[,c("tissue", "identity.super", "identity.sub", "identity.super.short", "identity.sub.short", "zfin")]
daniocell@meta.data <- cbind(daniocell@meta.data, daniocell.annot[daniocell@meta.data$cluster,])

# A function to re-generate the 'tissue subset' objects
# Usage: daniocell.tissue.subset(daniocell, tissue)
#    e.g. to recreate the axial mesoderm object: daniocell.tissue.subset(daniocell, "axial")
# Valid tissues are: blastomeres, periderm, axial, neural, hematopoietic, muscle, endoderm, pgc, eye, pronephros, 
#    glial, mesenchyme, epidermis, ionocytes, taste, otic, pigment, fin, mural
daniocell.tissue.subset <- function(daniocell, tissue) {
  if (!(tissue %in% names(daniocell@misc$tissue.umaps))) {
    message("The valid parameters for tissue are: ", paste0(names(daniocell@misc$tissue.umaps), collapse = ", "))
    stop("Please supply a valid tissue name.")
  }
  daniocell@reductions$umap@cell.embeddings <- as.matrix(daniocell@misc$tissue.umaps[[tissue]])
  cells.to.keep <- rownames(daniocell@meta.data)[daniocell@meta.data$subset.full == tissue]
  return(
    subset(daniocell, cells = cells.to.keep)
  )
}