writeCmd-2_function.R

dat_chr_cum <- function(dat, chr.cum.len) {
  dat$start <- 0
  dat$pos <- (dat$start + dat$size) / 2
  dat$chr <- factor(dat$chr, levels = names(chr.cum.len), ordered = T)
  dat$pos <- dat$pos + chr.cum.len[dat$chr]
  dat$chr <- as.character(dat$chr)
  return(dat)
}

areColors <- function(x) {
  sapply(x, function(y) {
    tryCatch(is.matrix(col2rgb(y)), error = function(e) FALSE)
  })
}

dat_dis_col <- function(i, dis_cols, dat) {
  dis_col <- dis_cols[i]
  dis_col <- gsub("\\s", "", strsplit(dis_col, ",")[[1]])
  dis_col <- gsub('\\"', "", dis_col)
  dis_col <- gsub("0x", "#", dis_col)
  if (length(dis_col) == 0) {
    dis_col <- NA
  }
  dat$color <- dis_col
  return(dat)
}

dat_cus_cols <- function(i, cus_cols, dat) {
  laycolor <- cus_cols[i]
  laycolor <- unlist(strsplit(laycolor, ";"))
  laycolor <- data.frame(id = laycolor, stringsAsFactors = F)
  laycolor$group <- gsub("\\:.*", "", laycolor$id)
  laycolor$cols <- gsub(".*\\:", "", laycolor$id)
  laycolor$group <- gsub(" ", "", laycolor$group)
  laycolor$cols <- gsub(" ", "", laycolor$cols)
  colname <- colnames(dat)
  dat <- merge(dat, laycolor, by.x = "color", by.y = "group", all.x = T)
  dat <- dat[c(colname, "cols")]
  return(dat)
}

lgd_mdy_label <- function(i, lgd_labels) {
  lgd_label <- gsub("\\s", "", strsplit(lgd_labels[i], ",")[[1]])
  lgd_label <- gsub('\\"', "", lgd_label)
  if (length(lgd_label) == 0) {
    lgd_label <- "NA"
  }
  return(lgd_label)
}

chr_cumsum <- function(dat, i) {
  chr.len <- dat$size
  names(chr.len) <- dat$chr
  if (i == 2) {
    chr.cum.len.tmp <<- c(0, cumsum(chr.len))
  }
  chr.cum.len <- c(0, cumsum(chr.len)[-length(chr.len)])
  names(chr.cum.len) <- names(chr.len)
  return(chr.cum.len)
}

cols_adjust <- function(i, dat, col_transpt, plot_type, type) {
  if ((type == 1 && (plot_type[i] %in% c("rect_discrete", "heatmap_discrete"))) |
      (type == 2 && (!plot_type[i] %in% c("point_gradual", "rect_gradual")))) {
    dat$color[!areColors(dat$color)] <- NA
    dat$color <- adjustcolor(dat$color, alpha.f = col_transpt[i])
    if (!all(is.na(dat$color))) {
      dat_val <- unique(dat$raw_color[!is.na(dat$raw_color)])
      dat_col <- dat$color[match(dat_val, dat$raw_color)]
    } else{
      dat_val <- unique(dat$raw_color[!is.na(dat$raw_color)])[1]
      dat_col <- "#FFFFFF00"
    }
  } else if (!plot_type[i] %in% c("heatmap_gradual", "heatmap_discrete", "text",
                                  "rect_gradual", "rect_discrete", "ideogram")){
    if (!"raw_color" %in% names(dat)) {
      dat$raw_color <- dat$color
    }
    if (!plot_type[i] %in% "segment") {
      dat_val <- unique(dat$raw_color[!is.na(dat$value)])
    } else{
      dat_val <- unique(dat$raw_color)
    }
    if (plot_type[i] %in% "vertical_line") {
      dat_val <- unique(dat$raw_color)
    }
    dat$color[!areColors(dat$color)] <- NA
    dat$color <- adjustcolor(dat$color, alpha.f = col_transpt[i])
    dat_col <- dat$color[match(dat_val, dat$raw_color)]
  }
  dat_val <- dat_val[!duplicated(dat_col)]
  dat_col <- dat_col[!duplicated(dat_col)]
  
  dat$raw_color <- factor(dat$raw_color, levels = dat_val, ordered = T)
  dat$color <- factor(dat$color, levels = dat_col, ordered = T)
  dat_val <<- dat_val[which(!dat_col %in% "#FFFFFF00")]
  dat_col <<- dat_col[!dat_col %in% "#FFFFFF00"]
  return(dat)
}

# the main function to make two genomes plot
two_genomes_plot <- function(data.chr1, data.chr2, data.2geno.plot, Height, Width, theme_sty, font_size, xtitle, ytitle, title_font_face, xlabel,
                             ylabel, lgd_pos, lgd_title_size, lgd_title_font_face, lgd_text_size, lgd_text_font_face, tc_chr_data1, tc_chr_data2, 
                             trackfil, plot_type, sel_gral_col, gral_col_tp, gral_2cols_ct, gral_3cols_ct, col_type, color_cus, color_mulgp,
                             col_transpt, symbol_point, symbol_point_type, point_size, point_size_type, line_size, vertical, vertical_col, 
                             vertical_size, vertical_type, horizontal, horizontal_col, horizontal_size, horizontal_type, add_border, border_col, 
                             linetype, col_lgd, col_lgd_name, size_lgd, size_lgd_name, shape_lgd, shape_lgd_name, col_lgd_mdy_label, col_lgd_label, 
                             size_lgd_mdy_label, size_lgd_label, shape_lgd_mdy_label, shape_lgd_label, laycolor.export) {
  
  ## *** Modify two genomes data ***
  names(data.chr1) <- c("chr", "size")
  data.chr1$size <- as.numeric(data.chr1$size)
  names(data.chr2) <- c("chr", "size")
  data.chr2$size <- as.numeric(data.chr2$size)
  tc_p1 <- ggplot()
  
  ## *** Plot theme ***
  tc_alltheme_sty <-
    list(
      theme_bw(), theme_classic(), theme_minimal(), theme_few(), theme_grey(), theme_tufte(),
      theme_calc(), theme_void(), theme_base(), theme_linedraw(), theme_economist(), theme_excel(),
      theme_fivethirtyeight(), theme_gdocs(), theme_hc(), theme_pander(), theme_solarized(), theme_wsj()
    )
  tc_p1 <- tc_p1 + tc_alltheme_sty[[as.numeric(gsub("theme", "", theme_sty))]]
  
  ## *** Modify main plot data ***
  if (plot_type %in% c("point_gradual", "point_discrete")) {
    names(data.2geno.plot)[1:4] <- c("chr1", "pos1", "chr2", "pos2")
    data.2geno.plot[c("pos1", "pos2")] <- sapply(data.2geno.plot[c("pos1", "pos2")], as.numeric)
    if(plot_type %in% "point_gradual"){
      data.2geno.plot[,5] <- as.numeric(data.2geno.plot[,5])
    }	
  }
  if (plot_type %in% c("segment", "rect_gradual", "rect_discrete")) {
    names(data.2geno.plot)[1:6] <- c("chr1", "xpos1", "xpos2", "chr2", "ypos1", "ypos2")
    data.2geno.plot[c("xpos1", "xpos2", "ypos1", "ypos2")] <- sapply(data.2geno.plot[c("xpos1", "xpos2", "ypos1", "ypos2")], as.numeric)
    if(plot_type %in% "rect_gradual"){
      data.2geno.plot[,7] <- as.numeric(data.2geno.plot[,7])
    }
  }
  
  ## *** Color ***
  if (plot_type %in% c("point_gradual", "rect_gradual")) {
    if (sel_gral_col == 1) {
      gralcols <- gsub('\\"', "", gral_col_tp)
    }else if(sel_gral_col == 2){
      gralcols <- gral_2cols_ct
    }else if (sel_gral_col == 3){
      gralcols <- gral_3cols_ct
    }
    gralcols <- unlist(strsplit(gralcols, "\\."))
  }
  
  if (plot_type %in% c("point_discrete", "segment", "rect_discrete")) {
    if (col_type == 2) {
      data.2geno.plot <- dat_dis_col(1, color_cus, data.2geno.plot)
    } else if (col_type == 3 & ("color" %in% colnames(data.2geno.plot))) {
      data.2geno.plot <- dat_cus_cols(1, color_mulgp, data.2geno.plot)
      laycolor <- unique(data.2geno.plot$cols)
      data.2geno.plot$raw_color <- data.2geno.plot$color
      data.2geno.plot$color <- data.2geno.plot$cols
      data.2geno.plot$cols <- NULL
    } else if (col_type == 1 & ("color" %in% colnames(data.2geno.plot))) {
      laycolor <- unlist(strsplit(laycolor.export, "\\."))
      laycolor <- data.frame(group = unique(data.2geno.plot$color), cols = laycolor, stringsAsFactors = F)
      colname <- colnames(data.2geno.plot)
      data.2geno.plot <- merge(data.2geno.plot, laycolor, by.x = "color", by.y = "group", all.x = T)
      data.2geno.plot <- data.2geno.plot[c(colname, "cols")]
      laycolor <- unique(data.2geno.plot$cols)
      data.2geno.plot$raw_color <- data.2geno.plot$color
      data.2geno.plot$color <- data.2geno.plot$cols
      data.2geno.plot$cols <- NULL
    } else{
      laycolor <- unlist(strsplit(laycolor.export, "\\."))
      data.2geno.plot$color <- laycolor
    }
  }
  
  ## *** The color labels ***
  if (!plot_type %in% c("point_gradual", "rect_gradual")) {
    if (!"raw_color" %in% names(data.2geno.plot)) {
      data.2geno.plot$raw_color <- data.2geno.plot$color
    }
    dat_val <<- NULL
    dat_col <<- NULL
    data.2geno.plot <- cols_adjust(1, data.2geno.plot, col_transpt, plot_type, 2)
    labelscol <- dat_val
    breakscol <- dat_col
  }
  
  ## *** Point type and size ***
  if (plot_type %in% c("point_gradual", "point_discrete")) {
    if (symbol_point_type == 1) {
      data.2geno.plot$shape <- as.numeric(symbol_point)
    } else if (symbol_point_type == 2 & (!"shape" %in% names(data.2geno.plot))) {
      data.2geno.plot$shape <- 16
    }
    if (point_size_type == 1) {
      data.2geno.plot$size <- as.numeric(point_size)
    } else if (point_size_type == 2 & (!"size" %in% names(data.2geno.plot))) {
      data.2geno.plot$size <- 0.8
    }
    breakspch <- unique(data.2geno.plot$shape)
    labelspch <- breakspch
    breakscex <- unique(data.2geno.plot$size)
    labelscex <- breakscex
  }
  
  ## *** Borders ***
  if (add_border == 2) {
    border_col <- NA
  }
  
  ## *** Legends ***
  add_col_lgd <- "none"; add_size_lgd <- "none"; add_shape_lgd <- "none"
  if (col_lgd == 1) {
    if (plot_type %in% c("point_gradual", "rect_gradual")) {
      add_col_lgd <- "colourbar"
    } else{
      add_col_lgd <- "legend"
    }
    if (plot_type %in% c("point_discrete", "segment", "rect_discrete")) {
      if (col_lgd_mdy_label == 1) {
        col_lgd_labelp <- lgd_mdy_label(1, col_lgd_label)
        col_lgd_labelp <- rep(col_lgd_labelp, length(breakscol))[1:length(breakscol)]
        names(col_lgd_labelp) <- labelscol
        data.2geno.plot$raw_color <- as.character(data.2geno.plot$raw_color)
        data.2geno.plot$raw_color <- col_lgd_labelp[data.2geno.plot$raw_color]
        labelscol <- unname(col_lgd_labelp)
        data.2geno.plot$raw_color <- factor(data.2geno.plot$raw_color, levels = unique(labelscol), ordered = T)
      }
    }
  }
  
  if (plot_type %in% c("point_gradual", "point_discrete")) {
    if (size_lgd == 1) {
      add_size_lgd <- "legend"
      if (size_lgd_mdy_label == 1) {
        size_lgd_labelp <- lgd_mdy_label(1, size_lgd_label)
        labelscex <- rep(size_lgd_labelp, length(breakscex))[1:length(breakscex)]
      }
    }
    if (shape_lgd == 1) {
      add_shape_lgd <- "legend"
      if (shape_lgd_mdy_label == 1) {
        shape_lgd_labelp <- lgd_mdy_label(1, shape_lgd_label)
        labelspch <- rep(shape_lgd_labelp, length(breakspch))[1:length(breakspch)]
      }
    }
  }
  
  ## *** The position of concatenated genome1 ***
  chr.cum.len <- chr_cumsum(data.chr1, 2)
  chr.cum.len_1 <- chr.cum.len.tmp
  
  data.chr1 <- dat_chr_cum(data.chr1, chr.cum.len)
  data.2geno.plot$chr1 <- factor(data.2geno.plot$chr1, levels = names(chr.cum.len), ordered = T)
  
  if (plot_type %in% c("segment", "rect_gradual", "rect_discrete")) {
    data.2geno.plot$xpos1 <- data.2geno.plot$xpos1 + chr.cum.len[data.2geno.plot$chr1]
    data.2geno.plot$xpos2 <- data.2geno.plot$xpos2 + chr.cum.len[data.2geno.plot$chr1]
  } else{
    data.2geno.plot$pos1 <- data.2geno.plot$pos1 + chr.cum.len[data.2geno.plot$chr1]
  }
  data.2geno.plot$chr1 <- as.character(data.2geno.plot$chr1)
  
  ## *** The position of concatenated genome2 ***
  chr.cum.len <- chr_cumsum(data.chr2, 2)
  chr.cum.len_2 <- chr.cum.len.tmp
  
  data.chr2 <- dat_chr_cum(data.chr2, chr.cum.len)
  data.2geno.plot$chr2 <- factor(data.2geno.plot$chr2, levels = names(chr.cum.len), ordered = T)
  
  if (plot_type %in% c("segment", "rect_gradual", "rect_discrete")) {
    data.2geno.plot$ypos1 <- data.2geno.plot$ypos1 + chr.cum.len[data.2geno.plot$chr2]
    data.2geno.plot$ypos2 <- data.2geno.plot$ypos2 + chr.cum.len[data.2geno.plot$chr2]
  } else{
    data.2geno.plot$pos2 <- data.2geno.plot$pos2 + chr.cum.len[data.2geno.plot$chr2]
  }
  data.2geno.plot$chr2 <- as.character(data.2geno.plot$chr2)
  
  ## *** Point_gradual ***
  if (plot_type == "point_gradual") {
    midpoint <- mean(data.2geno.plot$color, na.rm = T)
    if (is.numeric(labelscex)) {
      labelscex <- sprintf("%.1f", sort(labelscex))
    }
    if (is.numeric(labelspch)) {
      labelspch <- sort(labelspch)
    }
    if (lgd_pos == 1) {
      tc_p1 <- tc_p1 + geom_point(data = data.2geno.plot, aes(x = pos1, y = pos2, color = color, shape = as.character(shape), size = size))
      
      if(sel_gral_col == 2){
        tc_p1 <- tc_p1 + scale_color_gradient(name = col_lgd_name, guide = add_col_lgd, low = gralcols[1], high = gralcols[2], na.value = "#FFFFFF00")
      }else{
        tc_p1 <- tc_p1 + scale_color_gradient2(name = col_lgd_name, guide = add_col_lgd, low = gralcols[1], midpoint = midpoint, 
                                               mid = gralcols[2], high = gralcols[3], na.value = "#FFFFFF00")
      }
      
      tc_p1 <- tc_p1 + scale_size_identity(name = size_lgd_name, guide = add_size_lgd, breaks = sort(breakscex), labels = labelscex)
      tc_p1 <- tc_p1 + scale_shape_manual(name = shape_lgd_name, guide = add_shape_lgd, values = sort(breakspch), labels = labelspch)
      tc_p1 <- tc_p1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face), 
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
    } else{
      tc_p1 <- tc_p1 + geom_point(data = data.2geno.plot, aes(x = pos1, y = pos2, color = color, shape = as.character(shape), size = size))
      
      if(sel_gral_col == 2){
        tc_p1 <- tc_p1 + scale_color_gradient(name = col_lgd_name, guide = add_col_lgd, low = gralcols[1], high = gralcols[2], na.value = "#FFFFFF00")
      }else{          
        tc_p1 <- tc_p1 + scale_color_gradient2(name = col_lgd_name, guide = add_col_lgd, low = gralcols[1], midpoint = midpoint, 
                                               mid = gralcols[2], high = gralcols[3], na.value = "#FFFFFF00")
      }
      
      tc_p1 <- tc_p1 + scale_size_identity(name = size_lgd_name, guide = add_size_lgd, breaks = sort(breakscex), labels = labelscex)
      tc_p1 <- tc_p1 + scale_shape_manual(name = shape_lgd_name, guide = add_shape_lgd, values = sort(breakspch), labels = labelspch)
      tc_p1 <- tc_p1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face), 
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
    }
    if (add_col_lgd == "colourbar") {
      tc_p1 <- tc_p1 + guides(color = guide_colorbar(order = 1, title.vjust = 0.8, title.hjust = 0.4), size = guide_legend(order = 2))
    } else{
      tc_p1 <- tc_p1 + guides(size = guide_legend(order = 1))
    }
  }
  
  ## *** Point_discrete ***
  if (plot_type == "point_discrete") {
    if (is.numeric(labelscex)) {
      labelscex <- sprintf("%.1f", sort(labelscex))
    }
    if (is.numeric(labelspch)) {
      labelspch <- sort(labelspch)
    }
    if (lgd_pos == 1) {
      tc_p1 <- tc_p1 + geom_point(data = data.2geno.plot, aes(pos1, pos2, color = color, shape = as.character(shape), size = size))
      tc_p1 <- tc_p1 + scale_color_identity(name = col_lgd_name, guide = add_col_lgd, breaks = breakscol, labels = labelscol)
      tc_p1 <- tc_p1 + scale_size_identity(name = size_lgd_name, guide = add_size_lgd, breaks = sort(breakscex), labels = labelscex)
      tc_p1 <- tc_p1 + scale_shape_manual(name = shape_lgd_name, guide = add_shape_lgd, values = sort(breakspch), labels = labelspch)
      tc_p1 <- tc_p1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
      tc_p1 <- tc_p1 + guides(color = guide_legend(order = 1), size = guide_legend(order = 2))
    } else{
      tc_p1 <- tc_p1 + geom_point(data = data.2geno.plot, aes(pos1, pos2, color = color, shape = as.character(shape), size = size))
      tc_p1 <- tc_p1 + scale_color_identity(name = col_lgd_name, guide = add_col_lgd, breaks = breakscol, labels = labelscol)
      tc_p1 <- tc_p1 + scale_size_identity(name = size_lgd_name, guide = add_size_lgd, breaks = sort(breakscex), labels = labelscex)
      tc_p1 <- tc_p1 + scale_shape_manual(name = shape_lgd_name, guide = add_shape_lgd, values = sort(breakspch), labels = labelspch)
      tc_p1 <- tc_p1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
      tc_p1 <- tc_p1 + guides(color = guide_legend(order = 1), size = guide_legend(order = 2))
    }
  }
  
  ## *** Segment ***
  if (plot_type == "segment") {
    if (length(unique(data.2geno.plot$color)) > 1) {
      linetype <- "solid"
    }
    if (lgd_pos == 1) {
      tc_p1 <- tc_p1 + geom_segment(data = data.2geno.plot, aes(x = xpos1, y = ypos1, xend = xpos2, yend = ypos2, color = color),
                                    size = line_size, linetype = linetype)
      tc_p1 <- tc_p1 + scale_color_identity(name = col_lgd_name, guide = add_col_lgd, breaks = breakscol, labels = labelscol)
      tc_p1 <- tc_p1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
    } else{
      tc_p1 <- tc_p1 + geom_segment(data = data.2geno.plot, aes(x = xpos1, y = ypos1, xend = xpos2, yend = ypos2, color = color),
                                    size = line_size, linetype = linetype)
      tc_p1 <- tc_p1 + scale_color_identity(name = col_lgd_name, guide = add_col_lgd, breaks = breakscol, labels = labelscol)
      tc_p1 <- tc_p1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
    }
  }
  
  ## *** Rect_gradual ***
  if (plot_type == "rect_gradual") {
    midpoint <- mean(data.2geno.plot$color, na.rm = T)
    if (lgd_pos == 1) {
      tc_p1 <- tc_p1 + geom_rect(data = data.2geno.plot, aes(xmin = xpos1, xmax = xpos2, ymin = ypos1, ymax = ypos2, 
                                                             fill = color), color = border_col)
      
      if(sel_gral_col == 2){
        tc_p1 <- tc_p1 + scale_fill_gradient(name = col_lgd_name, guide = add_col_lgd, low = gralcols[1], high = gralcols[2], na.value = "#FFFFFF00")
      }else{
        tc_p1 <- tc_p1 + scale_fill_gradient2(name = col_lgd_name, guide = add_col_lgd, low = gralcols[1], midpoint = midpoint, 
                                              mid = gralcols[2], high = gralcols[3], na.value = "#FFFFFF00")
      }
      
      tc_p1 <- tc_p1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face), 
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
    } else{
      tc_p1 <- tc_p1 + geom_rect(data = data.2geno.plot, aes(xmin = xpos1, xmax = xpos2, ymin = ypos1, ymax = ypos2, fill = color), color = border_col)
      
      if(sel_gral_col == 2){
        tc_p1 <- tc_p1 + scale_fill_gradient(name = col_lgd_name, guide = add_col_lgd, low = gralcols[1], high = gralcols[2], na.value = "#FFFFFF00")
      }else{		  
        tc_p1 <- tc_p1 + scale_fill_gradient2(name = col_lgd_name, guide = add_col_lgd, low = gralcols[1], midpoint = midpoint, 
                                              mid = gralcols[2], high = gralcols[3], na.value = "#FFFFFF00")
      }
      
      tc_p1 <- tc_p1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face), 
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
      if(add_col_lgd != "none"){
        tc_p1 <- tc_p1 + guides(fill = guide_colourbar(title.vjust = 0.8, title.hjust = 0.4))
      }
    }
  }
  
  ## *** Rect_discrete ***
  if (plot_type == "rect_discrete") {
    if (lgd_pos == 1) {
      tc_p1 <- tc_p1 + geom_rect(data = data.2geno.plot, aes(xmin = xpos1, xmax = xpos2, ymin = ypos1, ymax = ypos2,
                                                             fill = color), color = border_col)
      tc_p1 <- tc_p1 + scale_fill_identity(name = col_lgd_name, guide = add_col_lgd, breaks = breakscol, labels = labelscol)
      tc_p1 <- tc_p1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
    } else{
      tc_p1 <- tc_p1 + geom_rect(data = data.2geno.plot, aes(xmin = xpos1, xmax = xpos2, ymin = ypos1, ymax = ypos2,
                                                             fill = color), color = border_col)
      tc_p1 <- tc_p1 + scale_fill_identity(name = col_lgd_name, guide = add_col_lgd, breaks = breakscol, labels = labelscol)
      tc_p1 <- tc_p1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
                             legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
    }
  }
  
  ## *** Vertical line ***
  if (vertical == 1) {
    tc_p1 <- tc_p1 + geom_vline(xintercept = chr.cum.len_1, linetype = vertical_type,
                                color = vertical_col, size = vertical_size)
  }
  
  ## *** Horizontal line ***
  if (horizontal == 1) {
    tc_p1 <- tc_p1 + geom_hline(yintercept = chr.cum.len_2, linetype = horizontal_type,
                                color = horizontal_col, size = horizontal_size)
  }
  
  ## *** The axis label ***
  if (xlabel == 1) {
    tc_p1 <- tc_p1 + scale_x_continuous(breaks = data.chr1$pos, labels = data.chr1$chr)
  } else{
    tc_p1 <- tc_p1 + theme(axis.text.x = element_blank(), axis.ticks.x = element_blank())
  }
  if (ylabel == 1) {
    tc_p1 <- tc_p1 + scale_y_continuous(breaks = data.chr2$pos, labels = data.chr2$chr)
  } else{
    tc_p1 <- tc_p1 + theme(axis.text.y = element_blank(), axis.ticks.y = element_blank())
  }
  
  ## *** The x and y axis title ***
  tc_p1 <- tc_p1 + xlab(xtitle) + ylab(ytitle)
  
  ## *** The font angle of axis title ***
  if (any(theme_sty %in% c("theme8", "theme16"))) {
    tc_p1 <- tc_p1 + theme(axis.title.x = element_text(hjust = 0.5, vjust = 1), axis.title.y = element_text(angle = 90, hjust = 0.5, vjust = 0.1))
  }
  
  ## *** Font face ***
  tc_p1 <- tc_p1 + theme(axis.title = element_text(face = title_font_face))
  
  ## *** Font size ***
  tc_p1 <- tc_p1 + theme(text = element_text(size = font_size))
  return(tc_p1)
}