--- a
+++ b/6-Figure scripts/Fig S3.R
@@ -0,0 +1,57 @@
+library(readxl)
+library(stringr)
+
+sheets <- excel_sheets("Fig S3 Source Data.xlsx")
+
+diseaseState <- c("COPD","Health")
+omics <- c("taxonomy","metagenome","metabolome","transcriptome","spu proteome","ser proteome")
+
+
+for(ds in diseaseState){
+  # ds=diseaseState[2]
+  
+  for(o in omics){
+    # o = omics[2]
+    s = sheets[grepl(ds, sheets) & grepl(o, sheets)]
+    
+    dat <- read_excel("Fig S3 Source Data.xlsx", sheet = s)
+    
+    for(Grp in c("Smoking", "ICS")){
+      # Grp = "Smoking"
+      dat.tmp <- dat 
+      if(!Grp %in% colnames(dat.tmp)) next
+      
+      if(Grp == "Smoking") Colors <- c("#E6194B","#3CB44B") else Colors <-c("#1ACDE5","#D8BA64")
+      
+      colnames(dat.tmp)[colnames(dat.tmp) == Grp] <- "Grp"
+      
+      dat.tmp$Grp <- as.factor(dat.tmp$Grp)
+      p<-ggplot(dat.tmp,aes(x=PC1,y=PC2))+
+        geom_point(aes(color = Grp)) +
+        scale_color_manual(values = Colors)+
+        scale_fill_manual(values = Colors)+
+        theme_bw()+ theme(panel.grid = element_blank(),
+                          legend.position = c(0.9, 0.85),
+                          legend.title = element_blank(),
+                          axis.text.x = element_blank(),
+                          axis.text.y = element_blank(),
+                          axis.ticks = element_blank())+
+        ggtitle(paste(str_to_title(o), ds, Grp,sep = " "))
+      p
+      assign(paste("P_",paste(c(o,ds,Grp),collapse = "."),sep = ""), p, envir = .GlobalEnv)
+    }
+  }
+}
+
+
+library(ggpubr)
+FigS3 <- 
+  ggarrange(
+    ggarrange(P_taxonomy.COPD.Smoking,P_taxonomy.Health.Smoking, P_taxonomy.COPD.ICS, ncol = 3),
+    ggarrange(P_metagenome.COPD.Smoking,P_metabolome.Health.Smoking, P_metagenome.COPD.ICS, ncol = 3),
+    ggarrange(P_metabolome.COPD.Smoking,P_metabolome.Health.Smoking,P_metabolome.COPD.ICS,ncol = 3),
+    ggarrange(P_transcriptome.COPD.Smoking,P_transcriptome.Health.Smoking,P_transcriptome.COPD.ICS,ncol = 3),
+    ggarrange(`P_spu proteome.COPD.Smoking`,`P_spu proteome.Health.Smoking`,`P_spu proteome.COPD.ICS`,ncol = 3),
+    ggarrange(`P_ser proteome.COPD.Smoking`,`P_ser proteome.Health.Smoking`,`P_ser proteome.COPD.ICS`,ncol = 3),
+    nrow = 6)
+FigS3
\ No newline at end of file