R/blank_genome.R

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

blank_genome = function(ref = "GRCh38", chromosomes = paste0('chr', c(1:22, 'X', 'Y')), label_chr = -0.5, cex = 1){
  reference_coordinates = get_reference(ref) %>%
    filter(chr %in% chromosomes)

  low = min(reference_coordinates$from)
  upp = max(reference_coordinates$to)


  #change the solid and dashed lines for better separating chromosomes.
  p1 = ggplot2::ggplot(reference_coordinates) +
    CNAqc:::my_ggplot_theme(cex = cex) +
    ggplot2::geom_segment(
      ggplot2::aes(
        x = centromerStart,
        xend = centromerEnd,
        y = 0,
        yend = Inf
      ),
      size = .1,
      color = 'black',
      linetype = 8
    )

  p1 = p1 + ggplot2::geom_rect(
    data = reference_coordinates,
    ggplot2::aes(
      xmin = from,
      xmax = from,
      ymin = 0,
      ymax = Inf
    ),
    alpha = 1,
    colour = 'grey',
  )

  p1 = p1 +
    ggplot2::geom_hline(yintercept = 0,
               size = 1,
               colour = 'gainsboro') +
    ggplot2::geom_hline(
      yintercept = 1,
      size = .3,
      colour = 'black',
      linetype = 'dashed'
    ) +
    ggplot2::labs(x = "Chromosome",
         y = "Major/ minor allele") +
    ggpubr::rotate_y_text() +
    # ggpubr::rotate_x_text() +
    # xlim(low, upp) +

    #set the chr names in the centromer positions.
    ggplot2::scale_x_continuous(
      breaks = c(0, reference_coordinates$centromerStart, upp),
      labels = c("", gsub(pattern = 'chr', replacement = '', reference_coordinates$chr), "")
    )

  return(p1)
}