Update 0_Compute_Zones.R

scripts/0_Compute_Zones.R

+# Note: The Matrix package version should be 1.6-4 or lower.
 library(Seurat)
 library(ggplot2)
 library(patchwork)
@@ -21,7 +22,7 @@ dir.create(path = out_dir, showWarnings = F)
 analysis_params <- list(
     min.feature = 500, # min nFeature_RNA
     max.pc.mito = 20, # max percent.mt
-    mito.prefix = "^mt-", # mito prefix
+    mito.prefix = "^mt-" # mito prefix
 )
 
 # Load Samples
@@ -90,7 +91,9 @@ DefaultAssay(crc.integrated) <- "integrated"
 plot1 <- FeatureScatter(crc.integrated, feature1 = 'nCount_SCT', feature2 = "nCount_Spatial", group.by = "orig.ident")
 plot2 <- FeatureScatter(crc.integrated,  feature1 = "nFeature_SCT", feature2 = "nCount_Spatial", group.by = "orig.ident")
 plot3 <- FeatureScatter(crc.integrated,  feature1 = "percent_mito", feature2 = "nFeature_Spatial", group.by = "orig.ident")
-CombinePlots(plots = list(plot1, plot2,plot3))
+png(filename = paste(out_dir, "IntegratedObj_QC.png", sep = "/"), width = 1200, height = 1000, res = 100)
+print(plot1 + plot2 + plot3)
+dev.off()
 # Scale data
 crc.integrated <- ScaleData(crc.integrated, verbose = FALSE)
 crc.integrated <- RunPCA(crc.integrated, npcs = 70, verbose = FALSE)