# ===================================================
# Load necessary libraries + custom theme ʕ⌐⧆ᴥ⧆ʔ
# ===================================================
library(ggplot2)
library(dplyr)
library(tidyr)
library(lubridate)
library(patchwork)

theme_pub <- ...

# ===================================================
# Data importing and check ʕ⌐⧇ᴥ⧇ʔ
# ===================================================
bf_meta <- read.csv('FOCO-BF-META.tsv', sep = "\t")
head(bf_meta)

# Define color palette
fly_colors <- c("#ef4444", "#f97316", "#f59e0b", "#eab308", "#84cc16", 
                "#22c55e", "#14b8a6", "#06b6d4", "#0ea5e9")

# Rename trap types
bf_meta$Trap.Type <- gsub("Lidded bait trap", "Carton trap", bf_meta$Trap.Type)
bf_meta$Trap.Type <- gsub("Baited net trap", "Net trap", bf_meta$Trap.Type)

# ===================================================
# Data visualization ʕ⌐⧮ᴥ⧮ʔ
# ===================================================
# Species distribution
species_plot <- ggplot(bf_meta, aes(x = reorder(Species, Species, function(x) length(x)), fill = reorder(Species, Species, function(x) length(x)))) +
  geom_bar() +
  coord_flip() +
  labs(y = "Count", x = "") +
  theme_pub() +
  theme(axis.text.y = element_text(size = 10),
        axis.text.x = element_text(),
        axis.title.y = element_blank(),
        legend.position = "none") +
  scale_y_continuous(expand = c(0, 0)) +
  scale_fill_manual(values = rev(fly_colors))

# Trap type effectiveness
trap_plot <- ggplot(bf_meta, aes(x = Trap.Type, fill = reorder(Species, Species, function(x) length(x)))) +
  geom_bar(position = "stack") +
  coord_flip() +
  labs(y = "Count", x = "") +
  theme_pub() +
  theme(
    legend.position = "none",
    axis.text.x.top = element_text(hjust = 0.5, margin = margin(b = 5), angle = 45),
    axis.text.y = element_text(face = "bold"),
    axis.title.x.top = element_blank(),
    axis.title.y = element_blank(),
    plot.margin = margin(r = 40)
  ) +
  scale_y_reverse(expand = c(0, 0)) +
  scale_x_discrete(position = "top") +
  scale_fill_manual(values = rev(fly_colors))

# Combine plots
combined_plot <- species_plot + trap_plot + 
  plot_layout(ncol = 2, widths = c(2, 1))

# Display combined plot
combined_plot

# Save the plot to a file
ggsave("FOCO-Flies-Combined-Plot.png", combined_plot, width = 10, height = 6, units = "in", dpi = 300)