library(vegan)
library(ggplot2)
library(ggpubr)
setwd("xxx")
df <- read.table("xxx", header = TRUE, row.names = 1)
df <- t(df)
shannon <- apply(df, 1, diversity)
data <- data.frame(sample = names(shannon), shannon = shannon)
metadata <- read.table("mother_metadata.txt", header = TRUE, row.names = 1)
data <- merge(data, metadata, by = "row.names", all.x = TRUE)
group_colors <- c("IC" = "#BD3C29", "RC" = "#0172B6", "OS" = "#78D3AC", "VS" = "#E18727")
compare_list <- list(
c("RC","VS"))
p <- ggplot(data, aes(x = group, y = shannon, fill = group, colour = group)) +
geom_boxplot(width = 0.5, alpha = 0.6, lwd = 1.15, outlier.shape = NA) +
geom_jitter(width = 0.3, size = 3, alpha = 0.75) +
labs(y = "Shannon Diversity") +
scale_fill_manual(values = group_colors) +
scale_color_manual(values = group_colors) +
theme_minimal() +
labs(x = NULL) +
theme(panel.border = element_rect(colour = "black", fill=NA, linewidth = 1.1)) +
stat_compare_means(
comparisons = compare_list,
method = "wilcox.test",
label = "p.signif",
hide.ns = TRUE)
ggsave("barplot.pdf", p, height = 5, width = 5)
