Telencephalon; Dorsomedial Telencephalic Nucleus (DMTN)

FindVariableFeatures(object = chromium_seurat, nfeatures = 3000)

ScaleData(object = chromium_seurat, split.by = "orig.ident",
do.center = FALSE)

RunOptimizeALS(object = chromium_seurat, k = 75, lambda = 5,
split.by = "orig.ident")

FindNeighbors(object = chromium_seurat_int, reduction = "iNMF_raw",
dims = 1:ncol(chromium_seurat_int[["iNMF_raw"]]), do.plot = FALSE)

FindClusters(object = chromium_seurat_int, resolution = res_values)

RunTSNE(object = chromium_seurat_int, tsne.method = "Rtsne",
dim.embed = 2, reduction = "iNMF_raw", dims = 1:ncol(chromium_seurat_int[["iNMF_raw"]]))

RunUMAP(object = chromium_seurat_int, metric = "cosine",
reduction = "iNMF_raw", n.components = 2, n.epochs = 500,