conversions.R

seurat_to_h5ad <- function(inputFile){
    library(Seurat)
    library(SeuratObject)
    library(SeuratDisk)

    outputFile <- gsub("\\.rds",".h5Seurat", inputFile)

    cat("\n-----------------------------------------------------------------------------\n")
    print(paste0("Conversion of the file ", inputFile))
    cat("\n-----------------------------------------------------------------------------\n")

    #' Load the Seurat Object
    cat("Load Seurat Object (SO)\n\n")
    SO <- readRDS(inputFile) 

    SO$phase <- Idents(SO)

    #' Save as a h5Seurat file format
    cat("Save SO as a h5Seurat file\n\n")
    SeuratDisk::SaveH5Seurat(SO, outputFile, overwrite = TRUE)

    #' Convert to a h5ad file format, readable by scanpy
    cat("Do the conversion from h5Seurat to h5ad file format\n\n")
    SeuratDisk::Convert(outputFile, dest = "h5ad", assay = "integrated", overwrite = TRUE)

    file.remove(outputFile)
}