Seurat has changed functions for reduced dims

[hypercompetent]

The current version of the make_seurat() function in clustering/clustering.R doesn't work on the current version of Seurat because of changes to Seurat functions. This version uses the updated CreateDimReducObject() function, and seems to work with what I've tested so far:

make_seurat = function(atac_matrix, metadata=NULL, pca_coords=NULL, tsne_coords=NULL) {
  if (is.null(pca_coords) && is.null(tsne_coords)) {
    stop('One of pca_coords or tsne_coords (or both) must be set to make the fake seurat object.')
  }
  
  if (!is.null(metadata)) {
    seurat_obj = CreateSeuratObject(atac_matrix, meta.data=metadata, project='DEFAULT', min.cells=0, min.features=0)
  } else {
    seurat_obj = CreateSeuratObject(atac_matrix, project='DEFAULT', min.cells=0, min.features=0)
  }
  
  if (!is.null(pca_coords)) {
    pca_coords = as.matrix(pca_coords)
    seurat_obj[["pca"]] <- CreateDimReducObject(embeddings = pca_coords,
                                                assay = DefaultAssay(object = seurat_obj),
                                                key = "PCA_")
  }
  
  if (!is.null(tsne_coords)) {
    tsne_coords = as.matrix(tsne_coords)
    seurat_obj[["tsne"]] <- CreateDimReducObject(embeddings = tsne_coords,
                                                 assay = DefaultAssay(object = seurat_obj),
                                                 key = "TSNE_")
    
  }
  
  return(seurat_obj)
}