R: 阿尔法α多样性计算和箱图制作，以及差异分析

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)