--- a
+++ b/src/SeuratToH5ad.R
@@ -0,0 +1,83 @@
+SeuratToH5ad <- function(seurat_object, filename, assay = NULL, res = 1) {
+  library(reticulate)
+  
+  if (!py_module_available("anndata") | !py_module_available("scanpy") | !py_module_available("igraph") | !py_module_available("louvain")) {
+    stop("Please install the anndata python module")
+  }
+  ad <- import("anndata")
+  sc <- import("scanpy")
+  
+  message(paste("Starting to fix the mess..."))
+  
+  raw <- seurat_object@assays$RNA@data
+  if (assay == "RNA") {
+    X <- seurat_object@assays$RNA@scale.data
+  } else if (assay == "SCT") {
+    X <- seurat_object@assays$SCT@scale.data
+  } else {
+    stop("Please select an existent assay")
+  }
+  
+  cell_names <- colnames(x = X)
+  gene_names <- rownames(x = X)
+  raw <- as(object = raw, Class = "dgCMatrix")
+  
+  scipy <- import(module = 'scipy.sparse', convert = FALSE)
+  sp_sparse_csc <- scipy$csc_matrix
+  raw.rownames <- rownames(x = raw)
+  raw <- sp_sparse_csc(
+    tuple(np_array(raw@x), np_array(raw@i), np_array(raw@p)),
+    shape = tuple(raw@Dim[1], raw@Dim[2])
+  )
+  
+  raw <- raw$T
+  raw <- dict(X = raw, var = dict(var_names = raw.rownames))
+  
+  X <- np_array(t(x = X))
+  
+  obsm <- list()
+  for (dr in names(seurat_object@reductions)) {
+    obsm[[paste0("X_",dr)]] <- np_array(Embeddings(
+      object = seurat_object,
+      reduction = dr
+    ))
+  }
+  obsm <- dict(obsm)
+  meta_data <- seurat_object@meta.data
+  if ("nCount_RNA" %in% colnames(x = meta_data)) {
+    colnames(x = meta_data) <- gsub(
+      pattern = "nCount_RNA",
+      replacement = "n_counts",
+      x = colnames(x = meta_data)
+    )
+  }
+  if ("nFeature_RNA" %in% colnames(x = meta_data)) {
+    colnames(x = meta_data) <- gsub(
+      pattern = "nFeature_RNA",
+      replacement = "n_genes",
+      x = colnames(x = meta_data)
+    )
+  }
+  colnames(x = meta_data) <- gsub(
+    pattern = "\\.",
+    replacement = "_",
+    x = colnames(x = meta_data)
+  )
+  
+  anndata.object <- ad$AnnData(
+    raw = raw,
+    X = X,
+    obs = meta_data,
+    obsm = obsm
+  )
+  anndata.object$var_names <- gene_names
+  anndata.object$obs_names <- cell_names
+  
+  #message(paste("Clustering for resolution:", res))
+  #sc$pp$neighbors(anndata.object)
+  #sc$tl$louvain(anndata.object, resolution=res, key_added = paste0("res", res))
+  
+  message(paste("Writing to h5ad file..."))
+  anndata.object$write(filename)
+  message(paste("Finished!!"))
+}
\ No newline at end of file