--- a
+++ b/6-Figure scripts/Fig S7.R
@@ -0,0 +1,65 @@
+library(readxl)
+
+excel_sheets("Fig S7 Source Data.xlsx")
+
+
+# Figure S7 a ----------------------------
+dat <- read_excel("Fig S7 Source Data.xlsx", sheet = "Shannon")
+head(dat)
+library(ggplot2)
+
+FigS7a <- ggplot(dat) +
+  geom_boxplot(aes(x=Group,y=Shannon,fill=Group),alpha=0.5,outlier.shape = NA) +
+  geom_jitter(aes(x=Group,y=Shannon,fill=Group),shape=21, width = 0.2,size=2) +
+  theme_bw() + theme(panel.grid = element_blank())+
+  xlab("") + ggtitle("Shannon index for \n K01426 contribution")
+
+# wilcox
+w=wilcox.test(Shannon~Group,data = dat)
+w$p.value  #0.006
+
+
+# Figure S7 b ----------------------------
+dat <- read_excel("Fig S7 Source Data.xlsx", sheet = "Contribution")
+colnames(dat)[1] <- "Species"
+
+library(RColorBrewer)
+nb.cols = 17
+mycolors <- colorRampPalette(brewer.pal(12, "Paired"))(nb.cols)
+library(scales)
+show_col(mycolors)
+
+
+# rank
+species_rank <- c(dat$Species[dat$Species != "Others"],"Others")
+
+
+dat <- reshape2::melt(dat, id.var="Species")
+dat$Species <- factor(dat$Species, levels = rev(species_rank))
+
+FigS7b <- ggplot(dat) +
+  geom_col(aes(x=variable,y=value,fill=Species))+
+  scale_fill_manual(values = c("gray",rev(mycolors)))+
+  theme_bw() + theme(panel.grid = element_blank())+
+  xlab("") + ylab("RPKM")+ ggtitle("Contribution to K01426")
+
+
+
+# Figure S7c ------------------------------------
+dat <- read_excel("Fig S7 Source Data.xlsx", sheet = "Differential contribution")
+colnames(dat)[1] <- "Species"
+
+library(ggrepel)
+FigS7c <- ggplot(dat) +
+  geom_point(aes(x=FC, y=log10P), size=2, alpha=0.5, fill="gray", shape=21)+
+  theme_bw() + theme(panel.grid = element_blank())+
+  geom_text_repel(aes(x=FC, y=log10P, label=Label)) +
+  geom_hline(yintercept = 1.3, color="red", size=0.3, linetype="dashed")+
+  geom_vline(xintercept = 0, color="darkgray", size=0.3, linetype="dashed")+
+  xlab("Fold-change of contribution to K01426") + ylab("minus log10 P-value") + 
+  ggtitle("Differential contribution to K01426")
+
+
+library(ggpubr)
+FigS7 <- ggarrange(FigS7a, FigS7b, FigS7c,ncol = 3)
+FigS7