Plots - VUmcCGP/wisecondor GitHub Wiki

A little explanation on the new style of plots:

• There is one blue line, showing the z-score per bin.
  -- The red line became obsolete due to removal of the windowed method and was removed.
• There is one way of marking aberrations.
  -- Orange is a fetal aberration, opacity is linearly determined by effect size up to 10%, at 10% the marking is opaque.
  -- Green is an aberration that, based on effect size (threshold at 20%), is likely maternal rather than fetal.
  -- The old purple/pink/green/lightgreen became obsolete due to removal of the windowed method and was removed.
• The number above/under an aberration shows the z-score for that aberration.
• Red/pink regions show bins that have no result due to lacking reference bins.
  -- Reasons vary from no reference genome information, barely mappable to no similar bins in the genome
• CytoBands can be added, see the arguments. No numbering is available, styling is close to the most common way cytobands are shown.

Although this is not a color scheme for maximum contrast, it allows colorblind people to recognize different colors in these plots. Additionally, the combination of these colors and removing several pieces of obsolete information from the plots makes the result easier on the eyes.