pca_plot <- function(
  eigenvector,
  eigenvalue,
  group,
  outdir,
  key = "pca",
  width = 8,
  height = 6,
  cexMain = 18,
  cexTick = 15,
  x_tick_angle = 0,
  x_tick_vjust = 0,
  add_lab = F,
  expand = c(0.02, 0.02)
){
  library(ggplot2)
  library(ggrepel)
  library(scales)
  setwd(outdir)
  the <- theme(#legend.position = "none",
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.border = element_blank(),
    panel.background = element_blank(),
    legend.title = element_blank(),
    legend.text = element_text(size = cexMain, face = "bold"),
    legend.key.height=unit(2,"line"),
    axis.title.x = element_text(face = "bold", size = cexMain, colour = "black"),
    axis.title.y = element_text(face = "bold", size = cexMain, colour = "black"),
    axis.text.x = element_text(size = cexTick,angle = x_tick_angle, vjust = x_tick_vjust, face = "bold", colour = "black"), 
    axis.text.y = element_text(face = "bold", size = cexTick, colour = "black"),
    axis.line.x = element_line(colour = "black", size = 1),
    axis.line.y = element_line(colour = "black", size = 1))
  egv <- read.table(eigenvector, header = T, stringsAsFactors = F)
  eva <- read.table(eigenvalue, header = T, stringsAsFactors = F)
  pop <- read.table(group, header = T, stringsAsFactors = F, check.names = F, comment.char = "")
  egv_order <- egv[match(pop[,3], egv[,1]),]
  pop_order <- pop[match(egv_order[,1], pop[,3]),]
  egv_order$group <- pop_order[,4]
  egv_order$group <- as.factor(egv_order$group)
  if(ncol(pop_order) == 5){
    egv_order$color <- pop_order[,5]
    col_df <- unique(pop_order[,4:5])
    col_df <- col_df[order(col_df[,1]),]
  }
  ### PC1 and PC2 plot
  p12 <- ggplot(data = egv_order)
  p12 <- p12 + geom_point(aes(x = PC1, y = PC2, group = group, color = group), size = 3, alpha = 1, shape = 19)
  if(add_lab == T){
    key <- paste0(key, ".label")
    p12 <- p12 + geom_text(vjust = -1, aes(x = PC1, y = PC2, label = sample))
  }
  if(ncol(pop_order) == 5){
    p12 <- p12 + scale_color_manual(labels = col_df$group, values = col_df$color)
  }
  p12 <- p12 + scale_x_continuous(breaks = pretty_breaks(5), expand = expand) 
  p12 <- p12 + scale_y_continuous(breaks = pretty_breaks(5), expand = expand)
  p12 <- p12 + xlab(paste0("PC1 (", round(eva[eva$PCs == "PC1", 3], 2), "%)"))
  p12 <- p12 + ylab(paste0("PC2 (", round(eva[eva$PCs == "PC2", 3], 2), "%)"))
  p12 <- p12 + theme_classic() + the
  if(length(unique(egv_order$group)) <= 1){
    p12 <- p12 + theme(legend.position = "none")
  }
  pdf(file = paste0(key, ".PC1_PC2.pdf"), width = width, height = height)
  print(p12)
  dev.off()
  png(filename = paste0(key, ".PC1_PC2.png"), width = width, height = height, units = "in", res = 300)
  print(p12)
  dev.off()
  
  ### PC1 and PC3 plot
  p13 <- ggplot(data = egv_order)
  p13 <- p13 + geom_point(aes(x = PC1, y = PC3, group = group, color = group), size = 3, alpha = 1, shape = 19)
  if(add_lab == T){
    p13 <- p13 + geom_text(vjust = -1, aes(x = PC1, y = PC3, label = sample))
  }
  if(ncol(pop_order) == 5){
    p13 <- p13 + scale_color_manual(labels = col_df$group, values = col_df$color)
  }
  p13 <- p13 + scale_x_continuous(breaks = pretty_breaks(5), expand = c(0.01, 0.01)) 
  p13 <- p13 + scale_y_continuous(breaks = pretty_breaks(5), expand = c(0.01, 0.01))
  p13 <- p13 + xlab(paste0("PC1 (", round(eva[eva$PCs == "PC1", 3], 2), "%)"))
  p13 <- p13 + ylab(paste0("PC3 (", round(eva[eva$PCs == "PC3", 3], 2), "%)"))
  p13 <- p13 + theme_classic() + the
  if(length(unique(egv_order$group)) <= 1){
    p13 <- p13 + theme(legend.position = "none")
  }
  pdf(file = paste0(key, ".PC1_PC3.pdf"), width = width, height = height)
  print(p13)
  dev.off()
  png(filename = paste0(key, ".PC1_PC3.png"), width = width, height = height, units = "in", res = 300)
  print(p13)
  dev.off()
  
  ### PC2 and PC3 plot
  p23 <- ggplot(data = egv_order)
  p23 <- p23 + geom_point(aes(x = PC2, y = PC3, group = group, color = group), size = 3, alpha = 1, shape = 19)
  if(add_lab == T){
    p23 <- p23 + geom_text(vjust = -1, aes(x = PC2, y = PC3, label = sample))
  }
  if(ncol(pop_order) == 5){
    p23 <- p23 + scale_color_manual(labels = col_df$group, values = col_df$color)
  }
  p23 <- p23 + scale_x_continuous(breaks = pretty_breaks(5), expand = c(0.01, 0.01)) 
  p23 <- p23 + scale_y_continuous(breaks = pretty_breaks(5), expand = c(0.01, 0.01))
  p23 <- p23 + xlab(paste0("PC2 (", round(eva[eva$PCs == "PC2", 3], 2), "%)"))
  p23 <- p23 + ylab(paste0("PC3 (", round(eva[eva$PCs == "PC3", 3], 2), "%)"))
  p23 <- p23 + theme_classic() + the
  if(length(unique(egv_order$group)) <= 1){
    p23 <- p23 + theme(legend.position = "none")
  }
  pdf(file = paste0(key, ".PC2_PC3.pdf"), width = width, height = height)
  print(p23)
  dev.off()
  png(filename = paste0(key, ".PC2_PC3.png"), width = width, height = height, units = "in", res = 300)
  print(p23)
  dev.off()
}