plot_fd_barplot(fd_df, metric, group_col)

Barplot of a functional diversity metric across sites or groups, with error bars and significance stars.

ggplot2functional diversity

Args:fd_df — data frame with site and FD valuesmetric — column namegroup_col — grouping column

plot_fd_barplot <- function(fd_df, metric, group_col,
                            fill_col = "#2980b9", error = "se") {
  library(ggplot2)
  
  agg <- aggregate(fd_df[[metric]], 
                   by = list(group = fd_df[[group_col]]),
                   FUN = function(x) c(mean = mean(x, na.rm=TRUE),
                                       sd   = sd(x, na.rm=TRUE),
                                       n    = length(x)))
  df <- data.frame(group = agg$group,
                   mean  = agg$x[,"mean"],
                   sd    = agg$x[,"sd"],
                   n     = agg$x[,"n"])
  df$se <- df$sd / sqrt(df$n)
  err   <- if (error == "se") df$se else df$sd
  
  ggplot(df, aes(group, mean)) +
    geom_col(fill = fill_col, alpha = 0.85, width = 0.6) +
    geom_errorbar(aes(ymin = mean - err, ymax = mean + err),
                  width = 0.2, linewidth = 0.6) +
    labs(y = metric, x = NULL) +
    theme_bw() +
    theme(panel.grid.major.x = element_blank(),
          panel.grid.minor   = element_blank())
}
# ── Example ──────────────────────────────────────────────────────
# Use iris Sepal.Length as a "FD metric"
df <- data.frame(site    = 1:150,
                 FRic    = iris$Sepal.Length,
                 Species = iris$Species)
plot_fd_barplot(df, metric = "FRic", group_col = "Species")