rm(list=ls()) 
library(bipartite)
library(betapart)
library(readxl)
library(fields)
library(ggplot2)
library(vegan)
library(pheatmap)
library(reshape2)
library(gridExtra)
library(grid)
install.packages("gridExtra")
# Read the matrix from the Excel file
ruta_archivo <- "data-METANETWORKS-QC.xlsx"  # Change to the path of your file
datos <- read_excel(ruta_archivo, sheet = "aggregated")  # Change "Hoja2" if necessary
# Convert all columns to numeric
datos[] <- lapply(datos, as.numeric)  
# Check if the conversion was successful
str(datos)
# Calculate beta diversity for the Chaco domain using Sørensen and Simpson indices with betapart
beta <- beta.pair(datos, index.family = "sorensen")
# Check that beta diversity was calculated correctly
print(beta$beta.sor)
print(beta$beta.sim)
print(beta$beta.sne)

# Convert the results to distance matrices
beta_sor_matrix <- as.matrix(beta$beta.sor)
beta_sim_matrix <- as.matrix(beta$beta.sim)
beta_sne_matrix <- as.matrix(beta$beta.sne)

# Assign site names to rows and columns
rownames(beta_sor_matrix) <- c("Chaco1", "Paraná1", "Chaco2", "Paraná2", "Chaco3", "Paraná3")
colnames(beta_sor_matrix) <- c("Chaco1", "Paraná1", "Chaco2", "Paraná2", "Chaco3", "Paraná3")

rownames(beta_sim_matrix) <- c("Chaco1", "Paraná1", "Chaco2", "Paraná2", "Chaco3", "Paraná3")
colnames(beta_sim_matrix) <- c("Chaco1", "Paraná1", "Chaco2", "Paraná2", "Chaco3", "Paraná3")

rownames(beta_sne_matrix) <- c("Chaco1", "Paraná1", "Chaco2", "Paraná2", "Chaco3", "Paraná3")
colnames(beta_sne_matrix) <- c("Chaco1", "Paraná1", "Chaco2", "Paraná2", "Chaco3", "Paraná3")

# Create each heatmap with smaller cells
p1 <- pheatmap(beta_sor_matrix, 
               main = "Beta-diversity (Sørensen Index)", 
               display_numbers = TRUE, 
               number_format = "%.2f",  # Number format with 2 decimals
               color = colorRampPalette(c("white", "lightyellow", "orange", "darkorange", "orangered"))(100), 
               cluster_rows = FALSE, 
               cluster_cols = FALSE,
               legend = TRUE, 
               silent = TRUE,
               fontsize_number = 8,  # Font size of numbers
               cellheight = 20,  # Adjust cell height
               cellwidth = 30)   # Adjust cell width

p2 <- pheatmap(beta_sim_matrix, 
               main = "Beta-diversity (Simpson Index)", 
               display_numbers = TRUE, 
               number_format = "%.2f",  # Number format with 2 decimals
               color = colorRampPalette(c("white", "lightyellow", "orange", "darkorange", "orangered"))(100), 
               cluster_rows = FALSE, 
               cluster_cols = FALSE,
               legend = TRUE, 
               silent = TRUE,
               fontsize_number = 8,  # Font size of numbers
               cellheight = 20,  # Adjust cell height
               cellwidth = 30)   # Adjust cell width

p3 <- pheatmap(beta_sne_matrix, 
               main = "Nestedness", 
               display_numbers = TRUE, 
               number_format = "%.2f",  # Number format with 2 decimals
               color = colorRampPalette(c("white", "lightyellow", "orange", "darkorange", "orangered"))(100), 
               cluster_rows = FALSE, 
               cluster_cols = FALSE,
               legend = TRUE, 
               silent = TRUE,
               fontsize_number = 8,  # Font size of numbers
               cellheight = 20,  # Adjust cell height
               cellwidth = 30)   # Adjust cell width

# Arrange the three plots in a single vertical panel
grid.arrange(p1$gtable, p2$gtable, p3$gtable, ncol = 1)

# Add a general title at the top
grid.text("Beta-diversity and Nestedness Analysis", 
          x = 0.5, y = 1, gp = gpar(fontsize = 14, fontface = "bold"))

# Save as PNG
png("Beta_Diversity_Interactions.png", width = 3000, height = 2200, res = 300)  # Adjust size and resolution
# Create each heatmap with smaller cells and individual titles with smaller font
p1 <- pheatmap(beta_sor_matrix, 
               main = "βsor", 
               display_numbers = TRUE, 
               number_format = "%.2f",  # Number format with 2 decimals
               color = colorRampPalette(c("white", "lightyellow", "orange", "darkorange", "orangered"))(100), 
               cluster_rows = FALSE, 
               cluster_cols = FALSE,
               legend = TRUE, 
               silent = TRUE,
               fontsize = 7,           # Reduce overall text size (including title)
               fontsize_number = 8,     # Font size of numbers
               cellheight = 20,         # Adjust cell height
               cellwidth = 30)          # Adjust cell width

p2 <- pheatmap(beta_sim_matrix, 
               main = "βsim", 
               display_numbers = TRUE, 
               number_format = "%.2f",  # Number format with 2 decimals
               color = colorRampPalette(c("white", "lightyellow", "orange", "darkorange", "orangered"))(100), 
               cluster_rows = FALSE, 
               cluster_cols = FALSE,
               legend = TRUE, 
               silent = TRUE,
               fontsize = 7,           # Reduce overall text size (including title)
               fontsize_number = 8,     # Font size of numbers
               cellheight = 20,         # Adjust cell height
               cellwidth = 30)          # Adjust cell width

p3 <- pheatmap(beta_sne_matrix, 
               main = "βsne", 
               display_numbers = TRUE, 
               number_format = "%.2f",  # Number format with 2 decimals
               color = colorRampPalette(c("white", "lightyellow", "orange", "darkorange", "orangered"))(100), 
               cluster_rows = FALSE, 
               cluster_cols = FALSE,
               legend = TRUE, 
               silent = TRUE,
               fontsize = 7,           # Reduce overall text size (including title)
               fontsize_number = 8,     # Font size of numbers
               cellheight = 20,         # Adjust cell height
               cellwidth = 30)          # Adjust cell width

# Arrange the three plots in a single vertical panel
grid.arrange(p1$gtable, p2$gtable, p3$gtable, ncol = 1)

# Add a general title at the top
grid.text("A)",
          x = 0.30, y = 0.95, gp = gpar(fontsize = 10, fontface = "bold"))
dev.off()


#### BIRDS

rm(list=ls()) 
library(bipartite)
library(betapart)
library(readxl)
library(fields)
library(ggplot2)
library(vegan)
library(pheatmap)
library(reshape2)
library(gridExtra)
library(grid)
install.packages("gridExtra")
# Read the matrix from the Excel file
ruta_archivo <- "data-birds.xlsx"  # Change to the path of your file
datos <- read_excel(ruta_archivo, sheet = "aggregated")  # Change "Hoja2" if necessary
# Convert all columns to numeric
datos[] <- lapply(datos, as.numeric)  
# Check if the conversion was successful
str(datos)
# Calculate beta diversity for the Chaco domain using Sørensen and Simpson indices with betapart
beta <- beta.pair(datos, index.family = "sorensen")
# Check that beta diversity was calculated correctly
print(beta$beta.sor)
print(beta$beta.sim)
print(beta$beta.sne)

# Load required libraries
library(pheatmap)

# Plot heatmap for Sørensen
pheatmap(beta$beta.sor, 
         main = "Beta-diversity (Sørensen Index)", 
         display_numbers = TRUE, 
         color = colorRampPalette(c("white", "blue"))(50),
         cluster_rows = TRUE, 
         cluster_cols = TRUE,
         legend = TRUE)

# Plot heatmap for Simpson
pheatmap(beta$beta.sim, 
         main = "Beta-diversity (Simpson Index)", 
         display_numbers = TRUE, 
         color = colorRampPalette(c("white", "red"))(50),
         cluster_rows = TRUE, 
         cluster_cols = TRUE,
         legend = TRUE)

# Plot heatmap for Nestedness
pheatmap(beta$beta.sne, 
         main = "Nestedness", 
         display_numbers = TRUE, 
         color = colorRampPalette(c("white", "green"))(50),
         cluster_rows = TRUE, 
         cluster_cols = TRUE,
         legend = TRUE)

# Convert the results to distance matrices
beta_sor_matrix <- as.matrix(beta$beta.sor)
beta_sim_matrix <- as.matrix(beta$beta.sim)
beta_sne_matrix <- as.matrix(beta$beta.sne)

# Assign site names to rows and columns
rownames(beta_sor_matrix) <- c("Chaco1", ...