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