R/addOncoprint.R

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

add_oncoprint = function(type, x, y, width, height, variant.classes, type_col) {
  for (i in 1:length(variant.classes)) {

    if (any(type %in% variant.classes[i])) {
      grid::grid.rect(x, y, width - unit(0.5, "mm"), height -
                        grid::unit(1, "mm"), gp = grid::gpar(col = NA, fill = type_col[variant.classes[i]]))
    } else if (any(type %in% 'Amp')) {
      grid::grid.rect(x, y, width - unit(0.5, "mm"), height -
                        grid::unit(1, "mm"), gp = grid::gpar(col = NA, fill = bg))
      grid::grid.rect(x, y, width - unit(0.5, "mm"), height -
                        unit(8, 'mm'), gp = grid::gpar(col = NA, fill = type_col['Amp']))
    } else if (any(type %in% 'Del')) {
      grid::grid.rect(x, y, width - unit(0.5, "mm"), height -
                        grid::unit(1, "mm"), gp = grid::gpar(col = NA, fill = bg))
      grid::grid.rect(x, y, width - unit(0.5, "mm"), height - grid::unit(8, "mm")
                      , gp = grid::gpar(col = NA, fill = type_col['Del']))
    }
  }

  if (any(type %in% "")) {
    grid::grid.rect(x, y, width - unit(0.5, "mm"), height -
                      grid::unit(1, "mm"), gp = grid::gpar(col = NA, fill = bg))
  }
}


add_oncoprint2 = function(type, x, y, width, height, variant.classes, type_col) {
  for (i in 1:length(variant.classes)) {

    if (any(type %in% variant.classes[i])) {
      grid::grid.rect(x, y, width - unit(0.5, "mm"), height -
                        grid::unit(1, "mm"), gp = grid::gpar(col = NA, fill = type_col[variant.classes[i]]))
    } else if (any(type %in% 'Amp')) {
      grid::grid.rect(x, y, width - unit(0.5, "mm"), height -
                        unit(8, 'mm'), gp = grid::gpar(col = NA, fill = type_col['Amp']))
    } else if (any(type %in% 'Del')) {

      grid::grid.rect(x, y, width - unit(0.5, "mm"), height - grid::unit(8, "mm")
                      , gp = grid::gpar(col = NA, fill = type_col['Del']))
    }
  }
}