1 files changed, 0 insertions, 92 deletions
diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
index cc087493..d637183d 100644
--- a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
@@ -370,95 +370,3 @@ lodchart = () ->
   
     # return the chart function
     chart
-
-
-# reorganize lod/pos by chromosome
-# lodvarname==null    -> case for multiple LOD columns (lodheatmap)
-# lodvarname provided -> case for one LOD column (lodchart)
-#reorgLodData = (data, lodvarname=null) ->
-#    data.posByChr = {}
-#    data.lodByChr = {}
-#    
-#    for chr,i in data.chrnames
-#      data.posByChr[chr[0]] = []
-#      data.lodByChr[chr[0]] = []
-#      for pos, j in data.pos
-#        if data.chr[j] == chr[0]
-#          data.posByChr[chr[0]].push(pos)
-#          data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)
-#          lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)
-#          data.lodByChr[chr[0]].push(lodval)
-#
-#
-#    if lodvarname?
-#      data.markers = []
-#      for marker,i in data.markernames
-#        if marker != ""
-#          data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]})
-#    
-#    data
-
-
-# calculate chromosome start/end + scales, for heat map
-#chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
-#    # start and end of chromosome positions
-#    chrStart = []
-#    chrEnd = []
-#    chrLength = []
-#    totalChrLength = 0
-#    maxd = 0
-#    for chr in data.chrnames
-#      d = maxdiff(data.posByChr[chr[0]])
-#      maxd = d if d > maxd
-#  
-#      rng = d3.extent(data.posByChr[chr[0]])
-#      chrStart.push(rng[0])
-#      chrEnd.push(rng[1])
-#      L = rng[1] - rng[0]
-#      chrLength.push(L)
-#      totalChrLength += L
-#  
-#    # adjust lengths for heatmap
-#    if pad4heatmap
-#      data.recwidth = maxd
-#      chrStart = chrStart.map (x) -> x-maxd/2
-#      chrEnd = chrEnd.map (x) -> x+maxd/2
-#      chrLength = chrLength.map (x) -> x+maxd
-#      totalChrLength += (chrLength.length*maxd)
-#  
-#    # break up x axis into chromosomes by length, with gaps
-#    data.chrStart = []
-#    data.chrEnd = []
-#    cur = leftMargin
-#    cur += chrGap/2 unless pad4heatmap
-#    data.xscale = {}
-#    for chr,i in data.chrnames
-#      data.chrStart.push(cur)
-#      w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i])
-#      data.chrEnd.push(cur + w)
-#      cur = data.chrEnd[i] + chrGap
-#      # x-axis scales, by chromosome
-#      data.xscale[chr[0]] = d3.scale.linear()
-#                           .domain([chrStart[i], chrEnd[i]])
-#                           .range([data.chrStart[i], data.chrEnd[i]])
-#  
-#    # return data with new stuff added
-#    data
-#    
-## maximum difference between adjacent values in a vector
-#maxdiff = (x) ->
-#    return null if x.length < 2
-#    result = x[1] - x[0]
-#    return result if x.length < 3
-#    for i in [2...x.length]
-#      d = x[i] - x[i-1]
-#      result = d if d > result
-#    result
-#    
-## determine rounding of axis labels
-#formatAxis = (d) ->
-#    d = d[1] - d[0]
-#    ndig = Math.floor( Math.log(d % 10) / Math.log(10) )
-#    ndig = 0 if ndig > 0
-#    ndig = Math.abs(ndig)
-#    d3.format(".#{ndig}f")