adding code for PDAC

scGPT/Redeconve/PDAC_Data_Formatting.R

@@ -16,3 +16,6 @@ rownames(dense_matrix) <- rownames(sc)  # Assign gene names to rows
 colnames(dense_matrix) <- colnames(sc)  # Assign spot names to columns
 
 write.csv(dense_matrix, file = "./PDAC/sc_data.csv", row.names = TRUE)
+
+
+

scGPT/Redeconve/Redeconve.R

@@ -51,5 +51,5 @@ annotations <- read.csv(paste0(data_folder, "./annotations.csv"))
 idx <- cell.sampling(ncells = 73260, annotations, size = 1000, prot = T)
 sc.ds <- sc[, idx[, 1]]
 
-res.ds <- deconvoluting(sc, st, genemode = "def", hpmode = "def", dopar = T, ncores = 32)
-write.csv(as.matrix(res.ds), "Redeconve.csv")
+res.ds <- deconvoluting(sc.ds, st, genemode = "def", hpmode = "def", dopar = T, ncores = 32)
+write.csv(as.matrix(res.ds), "Redeconve_lymph_node.csv")

scGPT/Redeconve/formatting_data.py

@@ -68,5 +68,34 @@ sp_data_human_lymph_node.var.to_csv(data_folder + "gene_names_sp_human_lymph_nod
 sp_data_human_lymph_node.obs.to_csv(data_folder + "cell_names_sp_human_lymph_nodes.csv", header=True, index=True)
 
 
+#### Below is Formatting the Result for PDAC ####
+
+data_folder = '../Generation_Result/'
+output_folder = "./PDAC/"
+tangram_result = sc.read_h5ad(data_folder + "scgpt_cell_reference_08_PDAC.h5ad")
+tangram_result.var_names_make_unique()
+
+
+# 读取scRNA结果文件
+sc_data_PDAC = sc.read_h5ad(data_folder + "adata_result_08_PDAC.h5ad")
+sc_data_PDAC.var_names_make_unique()
+
+
+# Save the sparse matrix (X) in Matrix Market format (.mtx)
+io.mmwrite(output_folder + "matrix_sc_PDAC_scGPT.mtx", sparse.csr_matrix(sc_data_PDAC.X))
+
+# Save gene names and cell names
+sc_data_PDAC.var.to_csv(output_folder + "gene_names_sc_PDAC.csv", header=True, index=True)
+sc_data_PDAC.obs.to_csv(output_folder + "cell_names_sc_PDAC.csv", header=True, index=True)
+
+# Save the sparse matrix (X) in Matrix Market format (.mtx)
+io.mmwrite(output_folder + "matrix_PDAC_tangram_result.mtx", sparse.csr_matrix(tangram_result.X))
+
+# Save gene names and cell names
+tangram_result.var.to_csv(output_folder + "gene_names_PDAC_tangram_result.csv", header=True, index=True)
+tangram_result.obs.to_csv(output_folder + "cell_names_PDAC_tangram_result.csv", header=True, index=True)
+
+
+