 
   # plug in -1 for nulls
   rf.forEach((cell) -> cell.value = -1 if cell.value is null)
-       
+
   # threshold the values and transform recombination fractions
-  rf.forEach((cell) -> 
+  rf.forEach((cell) ->
     cell.state = 0
     if cell.value is null
       cell.value = 0.5 if cell.row < cell.col

        cell.value = 0.5 if cell.value > 0.5
        cell.value = -4*(log2(cell.value)+1)/12*zmax
    cell.value = zmax if cell.value > zmax
  )    
        
  # the pixels
  cells = svg.selectAll(".cell")
      .data(rf)

# plot recombination fractions/LOD scores for all pairs of chromosomes

margin = {top: 100, right: 100, bottom: 100, left:100}
width = 720
height = 720
zmax = 12 # maximum LOD score

log2 = (x) -> Math.log(x)/Math.log(2.0)
onedigit = d3.format ".1f"

rf = []
chr = []
