add parts for cosine similarities

scGPT/Redeconve/PDAC.R

@@ -36,6 +36,7 @@ dir.create("./results")
 
 load("./PDAC/nums.RData")
 nums = as.matrix(nums)
+write.csv(nums, file="./PDAC/Redeconve_Result.csv", row.names=TRUE)
 #nums = deconvoluting(sc,st,gene.list = genes,hpmode = "cus",hp=10000,ncores=32)
 
 data_folder <- "./PDAC/"
@@ -44,6 +45,8 @@ data_folder <- "./PDAC/"
 sc_generated <- readMM(paste0(data_folder, "matrix_sc_PDAC_scGPT.mtx"))
 sc_generated <- t(sc_generated) # should be in dimension n_genes x n_cells
 
+
+
 # Load gene names and cell names
 gene_names <- read.csv(paste0(data_folder, "gene_names_sc_PDAC.csv"), header=FALSE, stringsAsFactors=FALSE)[,1][-1]
 cell_names <- read.csv(paste0(data_folder, "cell_names_sc_PDAC.csv"), header=FALSE, stringsAsFactors=FALSE)[,1]