plotting the results for pdac

scGPT/Redeconve/PDAC.R

@@ -135,7 +135,8 @@ dev.off()
 sc = sc_generated
 sc <- sc[common_genes, ]
 st <- st[common_genes, ]
-nums = deconvoluting(sc,st, genemode = "default", gene.list = common_genes, hpmode = "default", ncores=64)
+nums = deconvoluting(sc,st, genemode = "default", gene.list = common_genes, hpmode = "default", ncores=16)
+nums = as.matrix(nums)
 
 preexp = sc %*% nums 
 cossimr = matrix(nrow=428)
@@ -162,7 +163,8 @@ dev.off()
 
 sc <- sc[overlapped_marker, ]
 st <- st[overlapped_marker, ]
-nums = deconvoluting(sc,st, genemode = "default", gene.list = common_genes, hpmode = "default", ncores=64)
+nums = deconvoluting(sc,st, genemode = "default", gene.list = overlapped_marker, hpmode = "default", ncores=16)
+nums <- as.matrix(nums)
 
 preexp = sc %*% nums 
 cossimr = matrix(nrow=428)