Fixed a problem with the heatmap after moving reorgLodData function to panelutils.js

Got rqtl working with converted BXD genofile and also got composite mapping working

20 files changed, 1234 insertions, 704 deletions

diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 0433bf17..9b6b1b69 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -63,7 +63,14 @@ class Heatmap(object):
         

         self.all_sample_list = []

         self.traits = []

+        

+        chrnames = []

+        self.species = species.TheSpecies(dataset=self.trait_list[0][1])

+        for key in self.species.chromosomes.chromosomes.keys():

+            chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])

+        

         for trait_db in self.trait_list:

+                

             this_trait = trait_db[0]

             self.traits.append(this_trait.name)

             this_sample_data = this_trait.data

@@ -91,7 +98,7 @@ class Heatmap(object):
         self.gen_reaper_results()

         #self.gen_pylmm_results()

             

-        chrnames = []

+        #chrnames = []

         lodnames = []

         chr_pos = []

         pos = []

@@ -101,8 +108,9 @@ class Heatmap(object):
             lodnames.append(trait)

         

         for marker in self.dataset.group.markers.markers:

-            if marker['chr'] not in chrnames:

-                chrnames.append(marker['chr'])

+            #if marker['chr'] not in chrnames:

+            #    chr_ob = [marker['chr'], "filler"]

+            #    chrnames.append(chr_ob)

             chr_pos.append(marker['chr'])

             pos.append(marker['Mb'])

             markernames.append(marker['name'])

diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 4ac7bde2..e70f11cb 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -169,7 +169,12 @@ class IntervalMapping(object):
         self.json_data['markernames'] = []
         for qtl in reaper_results:
             reaper_locus = qtl.locus
-            self.json_data['chr'].append(reaper_locus.chr)
+            #if reaper_locus.chr == "20":
+            #    print("changing to X")
+            #    self.json_data['chr'].append("X")
+            #else:
+            #    self.json_data['chr'].append(reaper_locus.chr)
+            ##self.json_data['chr'].append(reaper_locus.chr)
             self.json_data['pos'].append(reaper_locus.Mb)
             self.json_data['lod.hk'].append(qtl.lrs)
             self.json_data['markernames'].append(reaper_locus.name)
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 648cb49b..59d87b36 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -12,6 +12,7 @@ import os
 import collections

 import uuid

 

+import rpy2.robjects as robjects

 import numpy as np

 from scipy import linalg

 

@@ -60,13 +61,20 @@ class MarkerRegression(object):
  

         self.mapping_method = start_vars['method']

         self.maf = start_vars['maf'] # Minor allele frequency

-        print("self.maf:", self.maf)

+        #print("self.maf:", self.maf)

  

         self.dataset.group.get_markers()

         if self.mapping_method == "gemma":

             qtl_results = self.run_gemma()

-        elif self.mapping_method == "rqtl":

-            qtl_results = self.run_rqtl()

+        elif self.mapping_method == "rqtl_plink":

+            qtl_results = self.run_rqtl_plink()

+        elif self.mapping_method == "rqtl_geno":

+            self.num_perm = start_vars['num_perm']

+            self.control = start_vars['control_marker']

+            self.control_db = start_vars['control_marker_db']

+            print("doing rqtl_geno")

+            qtl_results = self.run_rqtl_geno()

+            print("qtl_results:", qtl_results)

         elif self.mapping_method == "plink":

             qtl_results = self.run_plink()

             #print("qtl_results:", pf(qtl_results))

@@ -79,12 +87,14 @@ class MarkerRegression(object):
             

         self.lod_cutoff = 2    

         self.filtered_markers = []

+        highest_chr = 1 #This is needed in order to convert the highest chr to X/Y

         for marker in qtl_results:

             if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":

+                if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":

+                    highest_chr = marker['chr']

                 if 'lod_score' in marker:

                     self.filtered_markers.append(marker)

 

-

         self.json_data['chr'] = []

         self.json_data['pos'] = []

         self.json_data['lod.hk'] = []

@@ -94,7 +104,11 @@ class MarkerRegression(object):
         self.qtl_results = []

         for qtl in self.filtered_markers:

             print("lod score is:", qtl['lod_score'])

-            self.json_data['chr'].append(str(qtl['chr']))

+            if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":

+                print("changing to X")

+                self.json_data['chr'].append("X")

+            else:

+                self.json_data['chr'].append(str(qtl['chr']))

             self.json_data['pos'].append(qtl['Mb'])

             self.json_data['lod.hk'].append(str(qtl['lod_score']))

             self.json_data['markernames'].append(qtl['name'])

@@ -104,9 +118,10 @@ class MarkerRegression(object):
         self.json_data['chrnames'] = []

         for key in self.species.chromosomes.chromosomes.keys():

             self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])

-            

             chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length

         

+        print("json_data:", self.json_data)

+        

         self.js_data = dict(

             json_data = self.json_data,

             this_trait = self.this_trait.name,

@@ -186,7 +201,7 @@ class MarkerRegression(object):
     #

     #

     

-    def run_rqtl(self):

+    def run_rqtl_plink(self):

         os.chdir("/home/zas1024/plink")

         

         output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))

@@ -199,6 +214,103 @@ class MarkerRegression(object):
         

         count, p_values = self.parse_rqtl_output(plink_output_filename)

     

+    def run_rqtl_geno(self):

+        robjects.packages.importr("qtl")

+        robjects.r('the_cross <- read.cross(format="csvr", dir="/home/zas1024/PLINK2RQTL/test", file="BXD.csvr")')

+        robjects.r('the_cross <- calc.genoprob(the_cross)')

+        pheno_as_string = "c("

+        #for i, val in enumerate(self.vals):

+        #    if val == "x":

+        #        new_val == "NULL"

+        #    else:

+        #        new_val = val

+        #    if i < (len(self.vals) - 1):

+        #        pheno_as_string += str(new_val) + ","

+        #    else: pheno_as_string += str(new_val)

+        null_pos = []

+        for i, val in enumerate(self.vals):

+            if val == "x":

+                null_pos.append(i)

+                if i < (len(self.vals) - 1):

+                    pheno_as_string +=  "NA,"

+                else:

+                    pheno_as_string += "NA"

+            else:

+                if i < (len(self.vals) - 1):

+                    pheno_as_string += str(val) + ","

+                else:

+                    pheno_as_string += str(val)

+            

+        pheno_as_string += ")"

+        

+        print("self.control:", self.control)

+        if self.control != "":

+            print("self.control_db:", self.control_db)

+            control_trait = GeneralTrait(name=str(self.control), dataset_name=str(self.control_db))

+            control_vals = []

+            for sample in self.dataset.group.samplelist:

+                if sample in control_trait.data:

+                    control_vals.append(control_trait.data[sample].value)

+                else:

+                    control_vals.append("x")

+            print("control_vals:", control_vals)

+            control_as_string = "c("

+            for j, val2 in enumerate(control_vals):

+                if val2 == "x":

+                    if j < (len(control_vals) - 1):

+                        control_as_string +=  "NA,"

+                    else:

+                        control_as_string += "NA"

+                else:

+                    if j < (len(control_vals) - 1):

+                        control_as_string += str(val2) + ","

+                    else:

+                        control_as_string += str(val2)

+                #if i < (len(control_vals) - 1):

+                #    control_as_string += str(new_val2) + ","

+                #else:

+                #    control_as_string += str(new_val2)

+            control_as_string += ")"

+            print("control_as_string:", control_as_string)

+        

+            r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', n.perm='+self.num_perm+', addcovar='+control_as_string+')'

+            

+            if self.num_perm > 0:

+                thresholds = robjects.r(r_string)

+                print("thresholds:", thresholds)

+            

+            #r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', addcovar='+control_as_string+')'

+            print("r_string:", r_string)

+        else:

+        #r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', n.perm='+self.num_perm+')'

+            r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+')'

+            

+        print("r_string:", r_string)

+        result_data_frame = robjects.r(r_string)

+        #print("results:", result_data_frame)

+

+        qtl_results = self.process_rqtl_results(result_data_frame)

+        

+        return qtl_results

+    

+    def process_rqtl_results(self, result):

+        qtl_results = []

+        

+        output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]

+        print("output", output)

+        

+        

+        for i, line in enumerate(result.iter_row()):

+            marker = {}

+            marker['name'] = result.rownames[i]

+            marker['chr'] = output[i][0]

+            marker['Mb'] = output[i][1]

+            marker['lod_score'] = output[i][2]

+            

+            qtl_results.append(marker)

+            

+        return qtl_results

+

     def run_plink(self):

     

         os.chdir("/home/zas1024/plink")

@@ -271,6 +383,41 @@ class MarkerRegression(object):
             output_file.write(new_line)

             

         output_file.close()

+        

+    def gen_pheno_txt_file_rqtl(self, pheno_filename = ''):

+        ped_sample_list = self.get_samples_from_ped_file()	

+        output_file = open("%s%s.txt" % (webqtlConfig.TMPDIR, pheno_filename), "wb")

+        header = 'FID\tIID\t%s\n' % self.this_trait.name

+        output_file.write(header)

+    

+        new_value_list = []

+        

+        #if valueDict does not include some strain, value will be set to -9999 as missing value

+        for i, sample in enumerate(ped_sample_list):

+            try:

+                value = self.vals[i]

+                value = str(value).replace('value=','')

+                value = value.strip()

+            except:

+                value = -9999

+    

+            new_value_list.append(value)

+            

+            

+        new_line = ''

+        for i, sample in enumerate(ped_sample_list):

+            j = i+1

+            value = new_value_list[i]

+            new_line += '%s\t%s\t%s\n'%(sample, sample, value)

+            

+            if j%1000 == 0:

+                output_file.write(newLine)

+                new_line = ''

+        

+        if new_line:

+            output_file.write(new_line)

+            

+        output_file.close()

     

     # get strain name from ped file in order

     def get_samples_from_ped_file(self):

@@ -292,42 +439,6 @@ class MarkerRegression(object):
         

         return sample_list

     

-    ################################################################

-    # Generate Chr list, Chr OrderId and Retrieve Length Information 

-    ################################################################		

-    #def getChrNameOrderIdLength(self,RISet=''):

-    #    try:

-    #        query = """

-    #            Select

-    #                Chr_Length.Name,Chr_Length.OrderId,Length from Chr_Length, InbredSet

-    #            where

-    #                Chr_Length.SpeciesId = InbredSet.SpeciesId AND

-    #                InbredSet.Name = '%s' 

-    #            Order by OrderId

-    #            """ % (self.dataset.group.name)

-    #        results =g.db.execute(query).fetchall()

-    #        ChrList=[]

-    #        ChrLengthMbList=[]

-    #        ChrNameOrderIdDict={}

-    #        ChrOrderIdNameDict={}

-    #        

-    #        for item in results:

-    #            ChrList.append(item[0])

-    #            ChrNameOrderIdDict[item[0]]=item[1] # key is chr name, value is orderId

-    #            ChrOrderIdNameDict[item[1]]=item[0] # key is orderId, value is chr name

-    #            ChrLengthMbList.append(item[2])				

-    #            

-    #    except:

-    #        ChrList=[]

-    #        ChrNameOrderIdDict={}

-    #        ChrLengthMbList=[]

-    #        

-    #    return ChrList,ChrNameOrderIdDict,ChrOrderIdNameDict,ChrLengthMbList

-    

-    

-    def parse_rqtl_output(self, output_filename):

-        return True

-    

     def parse_plink_output(self, output_filename):

         plink_results={}

     

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 3034dec8..a4a24fd4 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -90,6 +90,10 @@ class ShowTrait(object):
 
         self.build_correlation_tools(self.this_trait)
 
+        #Get nearest marker for composite mapping
+        self.nearest_marker, self.nearest_marker_db = get_nearest_marker(self.this_trait)
+    
+
         self.make_sample_lists(self.this_trait)
 
         if self.dataset.group.allsamples:
@@ -101,6 +105,9 @@ class ShowTrait(object):
         hddn['method'] = "pylmm"
         hddn['mapping_display_all'] = True
         hddn['suggestive'] = 0
+        hddn['num_perm'] = 0
+        hddn['control_marker'] = self.nearest_marker
+        hddn['control_marker_db'] = self.nearest_marker_db
         hddn['maf'] = 0.01
         hddn['compare_traits'] = []
     
@@ -1267,3 +1274,21 @@ def get_samplelist_from_trait_data(this_trait, all_samples_ordered):
             other_sample_names.append(sample)
             
     return other_sample_names, all_samples_ordered
+
+def get_nearest_marker(this_trait):
+    this_chr = this_trait.chr
+    this_mb = this_trait.mb
+    query = """SELECT ProbeSet.Name, ProbeSetFreeze.Name
+               FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze
+               WHERE ProbeSet.Chr = '{}' AND
+                     ProbeSet.Id=ProbeSetXRef.ProbeSetId AND
+                     ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id AND
+                     ProbeSetFreeze.Name='{}'
+               ORDER BY ABS( Mb - {}) LIMIT 2""".format(this_trait.chr, this_trait.dataset.name, this_trait.mb)
+    print("query:", query)
+
+    result = g.db.execute(query).fetchall()
+
+    return result[1][0], result[1][1]
+    
+    
diff --git a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
index 2b4b20c8..c8e1b318 100644
--- a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
@@ -78,38 +78,3 @@ $("#export_pdf").click =>
     form.find("#data").val(svg_xml)

     form.find("#filename").val(filename)

     form.submit()

-

-# two LOD charts within one SVG

-#d3.json "data.json", (data) ->

-#  mychart_em = lodchart().lodvarname("lod.em")

-#                         .height(h)

-#                         .width(w)

-#                         .margin(margin)

-#                         .ylab("LOD score (by EM)")

-#                         .pointsize(1)

-#                         .nyticks(9)

-#                         .title("Standard interval mapping")

-#  mychart_hk = lodchart().lodvarname("lod.hk")

-#                         .height(h)

-#                         .width(w)

-#                         .margin(margin)

-#                         .ylab("LOD score (by H-K)")

-#                         .linecolor("Crimson")

-#                         .yticks([0, 1, 2, 4, 6, 8])

-#                         .title("Haley-Knott regression")

-#

-#  svg = d3.select("div#bottomchart")

-#          .append("svg")

-#          .attr("height", totalh)

-#          .attr("width", totalw)

-#

-#  chart1 = svg.append("g").attr("id", "chart1")

-#

-#  chart2 = svg.append("g").attr("id", "chart2")

-#              .attr("transform", "translate(0, #{halfh})")

-#

-#  chart1.datum(data)

-#    .call(mychart_em)

-#

-#  chart2.datum(data)

-#    .call(mychart_hk)
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee
index 6aa301a0..7831b2d4 100644
--- a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee
+++ b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee
@@ -90,8 +90,8 @@ iplotMScanone_noeff = (lod_data, times, chartOpts) ->
         lodchart_curves = g_lodchart.append("g").attr("id", "lodcurves")

         for chr in lod_data.chrnames

             lodchart_curves.append("path")

-                           .datum(lod_data.posByChr[chr])

-                           .attr("d", lodcurve(chr, lodcolumn))

+                           .datum(lod_data.posByChr[chr[0]])

+                           .attr("d", lodcurve(chr[0], lodcolumn))

                            .attr("stroke", linecolor)

                            .attr("fill", "none")

                            .attr("stroke-width", linewidth)

diff --git a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js
index e539d353..8f6787c3 100644
--- a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js
+++ b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js
@@ -68,7 +68,7 @@ iplotMScanone_noeff = function(lod_data, times, chartOpts) {
     _results = [];
     for (_i = 0, _len = _ref21.length; _i < _len; _i++) {
       chr = _ref21[_i];
-      _results.push(lodchart_curves.append("path").datum(lod_data.posByChr[chr]).attr("d", lodcurve(chr, lodcolumn)).attr("stroke", linecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none"));
+      _results.push(lodchart_curves.append("path").datum(lod_data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodcolumn)).attr("stroke", linecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none"));
     }
     return _results;
   };
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
index c9b277cc..dd2ad31d 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
@@ -39,7 +39,7 @@ lodchart = () ->
     chart = (selection) ->

       selection.each (data) ->

         

-        console.log("data:", data)

+        #console.log("data:", data)

         

         lodvarname = lodvarname ? data.lodnames[0]

         data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values

@@ -142,8 +142,8 @@ lodchart = () ->
 

   

         redraw_plot = (chr_ob) ->

-             console.log("chr_name is:", chr_ob[0])

-             console.log("chr_length is:", chr_ob[1])

+             #console.log("chr_name is:", chr_ob[0])

+             #console.log("chr_length is:", chr_ob[1])

              $('#topchart').remove()

              $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')

              chr_plot = new Chr_Interval_Map(600, 1200, chr_ob)

@@ -254,35 +254,34 @@ lodchart = () ->
               .x((d) -> xscale[chr](d))

               .y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn]))

               

-        #if data['additive'].length > 0

-        if 'additive' of data

-            additivecurve = (chr, lodcolumn) ->

-                d3.svg.line()

-                  .x((d) -> xscale[chr](d))

-                  .y((d,i) -> additive_yscale(data.additiveByChr[chr][i][lodcolumn]))

+        #if 'additive' of data

+        #    additivecurve = (chr, lodcolumn) ->

+        #        d3.svg.line()

+        #          .x((d) -> xscale[chr](d))

+        #          .y((d,i) -> additive_yscale(data.additiveByChr[chr][i][lodcolumn]))

   

         curves = g.append("g").attr("id", "curves")

   

-        #for chr in data.chrnames

-        #  curves.append("path")

-        #        .datum(data.posByChr[chr[0]])

-        #        .attr("d", lodcurve(chr[0], lodvarnum))

-        #        .attr("stroke", lodlinecolor)

-        #        .attr("fill", "none")

-        #        .attr("stroke-width", linewidth)

-        #        .style("pointer-events", "none")

+        for chr in data.chrnames

+          curves.append("path")

+                .datum(data.posByChr[chr[0]])

+                .attr("d", lodcurve(chr[0], lodvarnum))

+                .attr("stroke", lodlinecolor)

+                .attr("fill", "none")

+                .attr("stroke-width", linewidth)

+                .style("pointer-events", "none")

         

-        #if data['additive'].length > 0

-        if 'additive' of data

-            for chr in data.chrnames

-                curves.append("path")

-                      .datum(data.posByChr[chr[0]])

-                      .attr("d", additivecurve(chr[0], lodvarnum))

-                      .attr("stroke", additivelinecolor)

-                      .attr("fill", "none")

-                      .attr("stroke-width", 1)

-                      .style("pointer-events", "none")

-  

+        ##if data['additive'].length > 0

+        #if 'additive' of data

+        #    for chr in data.chrnames

+        #        curves.append("path")

+        #              .datum(data.posByChr[chr[0]])

+        #              .attr("d", additivecurve(chr[0], lodvarnum))

+        #              .attr("stroke", additivelinecolor)

+        #              .attr("fill", "none")

+        #              .attr("stroke-width", 1)

+        #              .style("pointer-events", "none")

+        #

         # points at markers

         if pointsize > 0

           markerpoints = g.append("g").attr("id", "markerpoints_visible")

diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index 0f91fc71..49ca962f 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -51,8 +51,7 @@ lodchart = function() {
   pointsAtMarkers = true;
   chart = function(selection) {
     return selection.each(function(data) {
-      var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis, _i, _len, _ref;
-      console.log("data:", data);
+      var additive_yaxis, chr, curves, g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis, _i, _len, _ref;
       lodvarname = lodvarname != null ? lodvarname : data.lodnames[0];
       data[lodvarname] = (function() {
         var _i, _len, _ref, _results;
@@ -128,8 +127,6 @@ lodchart = function() {
       xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).attr("fill", "slateblue").text(xlab);
       redraw_plot = function(chr_ob) {
         var chr_plot;
-        console.log("chr_name is:", chr_ob[0]);
-        console.log("chr_length is:", chr_ob[1]);
         $('#topchart').remove();
         $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
         return chr_plot = new Chr_Interval_Map(600, 1200, chr_ob);
@@ -185,22 +182,11 @@ lodchart = function() {
           return yscale(data.lodByChr[chr][i][lodcolumn]);
         });
       };
-      if ('additive' in data) {
-        additivecurve = function(chr, lodcolumn) {
-          return d3.svg.line().x(function(d) {
-            return xscale[chr](d);
-          }).y(function(d, i) {
-            return additive_yscale(data.additiveByChr[chr][i][lodcolumn]);
-          });
-        };
-      }
       curves = g.append("g").attr("id", "curves");
-      if ('additive' in data) {
-        _ref = data.chrnames;
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          chr = _ref[_i];
-          curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
-        }
+      _ref = data.chrnames;
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        chr = _ref[_i];
+        curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
       }
       if (pointsize > 0) {
         markerpoints = g.append("g").attr("id", "markerpoints_visible");
diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.coffee b/wqflask/wqflask/static/new/javascript/lodheatmap.coffee
index 6ffaefeb..5f3716bc 100644
--- a/wqflask/wqflask/static/new/javascript/lodheatmap.coffee
+++ b/wqflask/wqflask/static/new/javascript/lodheatmap.coffee
@@ -33,10 +33,14 @@ lodheatmap = () ->
             rectHeight = yscale(0)-yscale(1)

 

             xLR = {}

-            console.log("data.chrnames:", data.chrnames)

+            #console.log("data.posByChr:", data.posByChr["2"])

+            #console.log("data.chrnames:", data.chrnames)

             for chr in data.chrnames

-                console.log("chr is:", chr)

-                xLR[chr] = getLeftRight(data.posByChr[chr])

+                #console.log("posByChr:", data.posByChr)

+                #console.log("chr is:", chr)

+                xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]])

+      

+            #console.log("xLR:", xLR)

       

             # z-axis (color) limits; if not provided, make symmetric about 0

             zmin = 0

@@ -54,7 +58,9 @@ lodheatmap = () ->
             zthresh = zthresh ? zmin - 1

 

             data.cells = []

-            for chr in data.chrnames

+            for chr_ob in data.chrnames

+                chr = chr_ob[0]

+                #console.log("xLR[chr]:", xLR[chr])

                 for pos, i in data.posByChr[chr]

                     for lod,j in data.lodByChr[chr][i]

                         if lod >= zthresh or lod <= -zthresh

@@ -78,7 +84,7 @@ lodheatmap = () ->
              .data(data.chrnames)

              .enter()

              .append("rect")

-             .attr("id", (d) -> "box#{d}")

+             .attr("id", (d) -> "box#{d[0]}")

              .attr("x", (d,i) -> data.chrStart[i])

              .attr("y", (d) -> margin.top)

              .attr("height", height)

@@ -101,7 +107,7 @@ lodheatmap = () ->
                  .append("text")

                  .attr("x", (d,i) -> (data.chrStart[i] + data.chrEnd[i])/2)

                  .attr("y", margin.top+height+axispos.xlabel)

-                 .text((d) -> d)

+                 .text((d) -> d[0])

             xaxis.append("text").attr("class", "title")

                  .attr("x", margin.left+width/2)

                  .attr("y", margin.top+height+axispos.xtitle)

diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.js b/wqflask/wqflask/static/new/javascript/lodheatmap.js
index b009b4cd..5ea16590 100644
--- a/wqflask/wqflask/static/new/javascript/lodheatmap.js
+++ b/wqflask/wqflask/static/new/javascript/lodheatmap.js
@@ -33,7 +33,7 @@ lodheatmap = function() {
   cellSelect = null;
   chart = function(selection) {
     return selection.each(function(data) {
-      var cells, celltip, chr, extent, g, gEnter, i, j, lod, lodcol, nlod, pos, rectHeight, svg, titlegrp, xLR, xaxis, yaxis, zmax, zmin, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _m, _ref, _ref1, _ref2, _ref3, _ref4;
+      var cells, celltip, chr, chr_ob, extent, g, gEnter, i, j, lod, lodcol, nlod, pos, rectHeight, svg, titlegrp, xLR, xaxis, yaxis, zmax, zmin, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _m, _ref, _ref1, _ref2, _ref3, _ref4;
       data = reorgLodData(data);
       data = chrscales(data, width, chrGap, margin.left, true);
       xscale = data.xscale;
@@ -41,12 +41,10 @@ lodheatmap = function() {
       yscale.domain([-0.5, nlod - 0.5]).range([margin.top + height, margin.top]);
       rectHeight = yscale(0) - yscale(1);
       xLR = {};
-      console.log("data.chrnames:", data.chrnames);
       _ref = data.chrnames;
       for (_i = 0, _len = _ref.length; _i < _len; _i++) {
         chr = _ref[_i];
-        console.log("chr is:", chr);
-        xLR[chr] = getLeftRight(data.posByChr[chr]);
+        xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]);
       }
       zmin = 0;
       zmax = 0;
@@ -73,7 +71,8 @@ lodheatmap = function() {
       data.cells = [];
       _ref2 = data.chrnames;
       for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
-        chr = _ref2[_k];
+        chr_ob = _ref2[_k];
+        chr = chr_ob[0];
         _ref3 = data.posByChr[chr];
         for (i = _l = 0, _len3 = _ref3.length; _l < _len3; i = ++_l) {
           pos = _ref3[i];
@@ -98,7 +97,7 @@ lodheatmap = function() {
       svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom);
       g = svg.select("g");
       g.append("g").attr("id", "boxes").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
-        return "box" + d;
+        return "box" + d[0];
       }).attr("x", function(d, i) {
         return data.chrStart[i];
       }).attr("y", function(d) {
@@ -111,7 +110,7 @@ lodheatmap = function() {
       xaxis.selectAll("empty").data(data.chrnames).enter().append("text").attr("x", function(d, i) {
         return (data.chrStart[i] + data.chrEnd[i]) / 2;
       }).attr("y", margin.top + height + axispos.xlabel).text(function(d) {
-        return d;
+        return d[0];
       });
       xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab);
       rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
index 37226b8a..cc087493 100644
--- a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
@@ -32,8 +32,7 @@ lodchart = () ->
     ## the main function

     chart = (selection) ->

       selection.each (data) ->

-          

-        console.log("data:", data)

+        

           

         lodvarname = lodvarname ? data.lodnames[0]

         data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values

@@ -68,6 +67,8 @@ lodchart = () ->
         # if yticks not provided, use nyticks to choose pretty ones

         yticks = yticks ? yscale.ticks(nyticks)

   

+        console.log("data:", data)

+  

         # reorganize lod,pos by chromosomes

         data = reorgLodData(data, lodvarname)

   

@@ -206,7 +207,7 @@ lodchart = () ->
           markertip = d3.tip()

                         .attr('class', 'd3-tip')

                         .html((d) ->

-                          [d.name, " LRS = #{d3.format('.2f')(d.lod)}"])

+                          [d.name, " LOD = #{d3.format('.2f')(d.lod)}"])

                         .direction("e")

                         .offset([0,10])

           svg.call(markertip)

@@ -374,90 +375,90 @@ lodchart = () ->
 # 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

+#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")

+#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")

diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.js b/wqflask/wqflask/static/new/javascript/manhattan_plot.js
index 203f3a1b..9618acb2 100644
--- a/wqflask/wqflask/static/new/javascript/manhattan_plot.js
+++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.js
@@ -1,5 +1,5 @@
 // Generated by CoffeeScript 1.7.1
-var chrscales, formatAxis, lodchart, maxdiff, reorgLodData;
+var lodchart;
 
 lodchart = function() {
   var axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointhover, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
@@ -46,7 +46,6 @@ lodchart = function() {
   chart = function(selection) {
     return selection.each(function(data) {
       var g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, svg, titlegrp, x, xaxis, yaxis;
-      console.log("data:", data);
       lodvarname = lodvarname != null ? lodvarname : data.lodnames[0];
       data[lodvarname] = (function() {
         var _i, _len, _ref, _results;
@@ -67,6 +66,7 @@ lodchart = function() {
       g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none");
       yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]);
       yticks = yticks != null ? yticks : yscale.ticks(nyticks);
+      console.log("data:", data);
       data = reorgLodData(data, lodvarname);
       data = chrscales(data, width, chrGap, margin.left, pad4heatmap);
       xscale = data.xscale;
@@ -138,7 +138,7 @@ lodchart = function() {
       if (pointsAtMarkers) {
         hiddenpoints = g.append("g").attr("id", "markerpoints_hidden");
         markertip = d3.tip().attr('class', 'd3-tip').html(function(d) {
-          return [d.name, " LRS = " + (d3.format('.2f')(d.lod))];
+          return [d.name, " LOD = " + (d3.format('.2f')(d.lod))];
         }).direction("e").offset([0, 10]);
         svg.call(markertip);
         return markerSelect = hiddenpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
@@ -339,137 +339,3 @@ lodchart = function() {
   };
   return chart;
 };
-
-reorgLodData = function(data, lodvarname) {
-  var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2;
-  if (lodvarname == null) {
-    lodvarname = null;
-  }
-  data.posByChr = {};
-  data.lodByChr = {};
-  _ref = data.chrnames;
-  for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
-    chr = _ref[i];
-    data.posByChr[chr[0]] = [];
-    data.lodByChr[chr[0]] = [];
-    _ref1 = data.pos;
-    for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {
-      pos = _ref1[j];
-      if (data.chr[j] === chr[0]) {
-        data.posByChr[chr[0]].push(pos);
-        if (!Array.isArray(data.lodnames)) {
-          data.lodnames = [data.lodnames];
-        }
-        lodval = (function() {
-          var _k, _len2, _ref2, _results;
-          _ref2 = data.lodnames;
-          _results = [];
-          for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
-            lodcolumn = _ref2[_k];
-            _results.push(data[lodcolumn][j]);
-          }
-          return _results;
-        })();
-        data.lodByChr[chr[0]].push(lodval);
-      }
-    }
-  }
-  if (lodvarname != null) {
-    data.markers = [];
-    _ref2 = data.markernames;
-    for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) {
-      marker = _ref2[i];
-      if (marker !== "") {
-        data.markers.push({
-          name: marker,
-          chr: data.chr[i],
-          pos: data.pos[i],
-          lod: data[lodvarname][i]
-        });
-      }
-    }
-  }
-  return data;
-};
-
-chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
-  var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;
-  chrStart = [];
-  chrEnd = [];
-  chrLength = [];
-  totalChrLength = 0;
-  maxd = 0;
-  _ref = data.chrnames;
-  for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-    chr = _ref[_i];
-    d = maxdiff(data.posByChr[chr[0]]);
-    if (d > maxd) {
-      maxd = d;
-    }
-    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;
-  }
-  if (pad4heatmap) {
-    data.recwidth = maxd;
-    chrStart = chrStart.map(function(x) {
-      return x - maxd / 2;
-    });
-    chrEnd = chrEnd.map(function(x) {
-      return x + maxd / 2;
-    });
-    chrLength = chrLength.map(function(x) {
-      return x + maxd;
-    });
-    totalChrLength += chrLength.length * maxd;
-  }
-  data.chrStart = [];
-  data.chrEnd = [];
-  cur = leftMargin;
-  if (!pad4heatmap) {
-    cur += chrGap / 2;
-  }
-  data.xscale = {};
-  _ref1 = data.chrnames;
-  for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) {
-    chr = _ref1[i];
-    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;
-    data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
-  }
-  return data;
-};
-
-maxdiff = function(x) {
-  var d, i, result, _i, _ref;
-  if (x.length < 2) {
-    return null;
-  }
-  result = x[1] - x[0];
-  if (x.length < 3) {
-    return result;
-  }
-  for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) {
-    d = x[i] - x[i - 1];
-    if (d > result) {
-      result = d;
-    }
-  }
-  return result;
-};
-
-formatAxis = function(d) {
-  var ndig;
-  d = d[1] - d[0];
-  ndig = Math.floor(Math.log(d % 10) / Math.log(10));
-  if (ndig > 0) {
-    ndig = 0;
-  }
-  ndig = Math.abs(ndig);
-  return d3.format("." + ndig + "f");
-};
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.coffee b/wqflask/wqflask/static/new/javascript/panelutil.coffee
new file mode 100644
index 00000000..d1eb83e5
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/panelutil.coffee
@@ -0,0 +1,357 @@
+# A variety of utility functions used by the different panel functions

+

+# determine rounding of axis labels

+formatAxis = (d, extra_digits=0) ->

+    d = d[1] - d[0]

+    ndig = Math.floor( Math.log(d % 10) / Math.log(10) )

+    ndig = 0 if ndig > 0

+    ndig = Math.abs(ndig) + extra_digits

+    d3.format(".#{ndig}f")

+

+# unique values of array (ignore nulls)

+unique = (x) ->

+    output = {}

+    output[v] = v for v in x when v

+    output[v] for v of output

+

+# Pull out a variable (column) from a two-dimensional array

+pullVarAsArray = (data, variable) ->

+    v = []

+    for i of data

+        v = v.concat data[i][variable]

+    v

+  

+  

+# 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

+      #console.log("chr:", chr)

+      data.posByChr[chr[0]] = []

+      data.lodByChr[chr[0]] = []

+      for pos, j in data.pos

+        if data.chr[j].toString() == chr[0]

+          #console.log(data.chr[j] + " AND " + 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)

+

+    #console.log("data.posByChr:", data.posByChr)

+

+    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

+    

+    

+# 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 = {}

+#

+#    #console.log("data.chr", data.chr)

+#    #console.log("data.chrnames:", data.chrnames)

+#    the_chr = "0"

+#    for chr,i in data.chrnames

+#        data.posByChr[chr] = []

+#        data.lodByChr[chr] = []

+#        for pos,j in data.pos

+#            console.log("data.chr[j][0]:", data.chr[j][0])

+#            if data.chr[j][0] == chr

+#                console.log("IS EQUAL")

+#                data.posByChr[chr].push(pos)

+#                data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)

+#                lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)

+#                data.lodByChr[chr].push(lodval)

+#

+#    if lodvarname?

+#        data.markers = []

+#        for marker,i in data.markernames

+#            if marker != ""

+#                data.markers.push({name:marker, chr:data.chr[i][0], 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])

+#        maxd = d if d > maxd

+#

+#        rng = d3.extent(data.posByChr[chr])

+#        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] = d3.scale.linear()

+#                             .domain([chrStart[i], chrEnd[i]])

+#                             .range([data.chrStart[i], data.chrEnd[i]])

+#

+#    # return data with new stuff added

+#    data

+

+# Select a set of categorical colors

+# ngroup is positive integer

+# palette = "dark" or "pastel"

+selectGroupColors = (ngroup, palette) ->

+    return [] if ngroup == 0

+

+    if palette == "dark"

+        return ["slateblue"] if ngroup == 1

+        return ["MediumVioletRed", "slateblue"] if ngroup == 2

+        return colorbrewer.Set1[ngroup] if ngroup <= 9

+        return d3.scale.category20().range()[0...ngroup]

+    else

+        return ["#bebebe"] if ngroup == 1

+        return ["lightpink", "lightblue"] if ngroup == 2

+        return colorbrewer.Pastel1[ngroup] if ngroup <= 9

+        # below is rough attempt to make _big_ pastel palette

+        return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8",

+                "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6",

+                "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4",

+                "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7",

+                "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"][0...ngroup]

+

+# expand element/array (e.g., of colors) to a given length

+#     single elment -> array, then repeated to length n

+expand2vector = (input, n) ->

+    return input unless input? # return null if null

+    return input if Array.isArray(input) and input.length >= n

+    input = [input] unless Array.isArray(input)

+    input = (input[0] for i of d3.range(n)) if input.length == 1 and n > 1

+    input

+

+# median of a vector

+median = (x) ->

+    return null if !x? 

+    n = x.length

+    x.sort((a,b) -> a-b)

+    if n % 2 == 1

+        return x[(n-1)/2]

+    (x[n/2] + x[(n/2)-1])/2

+

+# given a vector of x's, return hash with values to left and right, and the differences

+getLeftRight = (x) ->

+    n = x.length

+    x.sort( (a,b) -> a-b )

+

+    xdif = []

+    result = {}

+    for v in x

+        result[v] = {}

+

+    for i in [1...n]

+        #console.log("result:", result)

+        xdif.push(x[i]-x[i-1])

+        result[x[i]].left = x[i-1]

+    for i in [0...(n-1)]

+        result[x[i]].right = x[i+1]

+

+    xdif = median(xdif)

+    result.mediandiff = xdif

+

+    result[x[0]].left = x[0]-xdif

+    result[x[n-1]].right = x[n-1]+xdif

+    result.extent = [x[0]-xdif/2, x[n-1]+xdif/2]

+

+    result

+

+# 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

+

+# matrix extent, min max

+matrixMin = (mat) ->

+    result = mat[0][0]

+    for i of mat

+        for j of mat[i]

+            result = mat[i][j] if result > mat[i][j]

+    result      

+

+matrixMax = (mat) ->

+    result = mat[0][0]

+    for i of mat

+        for j of mat[i]

+            result = mat[i][j] if result < mat[i][j]

+    result      

+

+matrixMaxAbs = (mat) ->

+    result = Math.abs(mat[0][0])

+    for i of mat

+        for j of mat[i]

+            result = Math.abs(mat[i][j]) if result < mat[i][j]

+    result      

+

+matrixExtent = (mat) -> [matrixMin(mat), matrixMax(mat)]

+

+d3.selection.prototype.moveToFront = () ->

+    this.each () -> this.parentNode.appendChild(this)

+  

+d3.selection.prototype.moveToBack = () ->

+    this.each () ->

+        firstChild = this.parentNode.firstchild

+        this.parentNode.insertBefore(this, firstChild) if firstChild

+

+forceAsArray = (x) ->

+    return x unless x? # if null, return null

+    return x if Array.isArray(x)

+    [x]

+

+# any values in vec that appear in missing are made null

+missing2null = (vec, missingvalues=['NA', '']) ->

+    vec.map (value) -> if missingvalues.indexOf(value) > -1 then null else value

+

+# display error at top of page

+displayError = (message) ->

+    if d3.select("div.error").empty() # no errors yet

+        d3.select("body")

+          .insert("div", ":first-child")

+          .attr("class", "error")

+    d3.select("div.error")

+      .append("p")

+      .text(message)

+

+# sum values in an array

+sumArray = (vec) -> (vec.reduce (a,b) -> a+b)

+

+# calculate cross-tabulation

+calc_crosstab = (data) ->

+    nrow = data.ycat.length

+    ncol = data.xcat.length

+

+    result = ((0 for col in [0..ncol]) for row in [0..nrow]) # matrix of 0's

+

+    # count things up

+    for i of data.x

+        result[data.y[i]][data.x[i]] += 1

+

+    # row and column sums

+    rs = rowSums(result)

+    cs = colSums(result)

+

+    # fill in column sums

+    for i in [0...ncol]

+        result[nrow][i] = cs[i]

+

+    # fill in row sums

+    for i in [0...nrow]

+        result[i][ncol] = rs[i]

+

+    # fill in total

+    result[nrow][ncol] = sumArray(rs)

+

+    result

+

+# rowSums: the sums for each row

+rowSums = (mat) -> (sumArray(x) for x in mat)

+

+# transpose: matrix transpose

+transpose = (mat) -> ((mat[i][j] for i in [0...mat.length]) for j in [0...mat[0].length])

+

+# colSums = the sums for each column

+colSums = (mat) -> rowSums(transpose(mat))

+

+# log base 2

+log2 = (x) -> 

+    return(x) unless x?

+    Math.log(x)/Math.log(2.0)

+

+# log base 10

+log10 = (x) ->

+    return(x) unless x?

+    Math.log(x)/Math.log(10.0)

+

+# absolute value, preserving nulls

+abs = (x) -> 

+    return(x) unless x?

+    Math.abs(x)
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js
index 07384f2b..2acc1651 100644
--- a/wqflask/wqflask/static/new/javascript/panelutil.js
+++ b/wqflask/wqflask/static/new/javascript/panelutil.js
@@ -1,319 +1,439 @@
-// Generated by CoffeeScript 1.7.1

-var chrscales, expand2vector, forceAsArray, formatAxis, getLeftRight, matrixExtent, matrixMax, matrixMaxAbs, matrixMin, maxdiff, median, pullVarAsArray, reorgLodData, selectGroupColors, unique;

-

-formatAxis = function(d) {

-  var ndig;

-  d = d[1] - d[0];

-  ndig = Math.floor(Math.log(d % 10) / Math.log(10));

-  if (ndig > 0) {

-    ndig = 0;

-  }

-  ndig = Math.abs(ndig);

-  return d3.format("." + ndig + "f");

-};

-

-unique = function(x) {

-  var output, v, _i, _len, _results;

-  output = {};

-  for (_i = 0, _len = x.length; _i < _len; _i++) {

-    v = x[_i];

-    if (v) {

-      output[v] = v;

-    }

-  }

-  _results = [];

-  for (v in output) {

-    _results.push(output[v]);

-  }

-  return _results;

-};

-

-pullVarAsArray = function(data, variable) {

-  var i, v;

-  v = [];

-  for (i in data) {

-    v = v.concat(data[i][variable]);

-  }

-  return v;

-};

-

-reorgLodData = function(data, lodvarname) {

-  var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2;

-  if (lodvarname == null) {

-    lodvarname = null;

-  }

-  data.posByChr = {};

-  data.lodByChr = {};

-  _ref = data.chrnames;

-  for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {

-    chr = _ref[i];

-    data.posByChr[chr] = [];

-    data.lodByChr[chr] = [];

-    _ref1 = data.pos;

-    for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {

-      pos = _ref1[j];

-      if (data.chr[j] === chr) {

-        data.posByChr[chr].push(pos);

-        if (!Array.isArray(data.lodnames)) {

-          data.lodnames = [data.lodnames];

-        }

-        lodval = (function() {

-          var _k, _len2, _ref2, _results;

-          _ref2 = data.lodnames;

-          _results = [];

-          for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {

-            lodcolumn = _ref2[_k];

-            _results.push(data[lodcolumn][j]);

-          }

-          return _results;

-        })();

-        data.lodByChr[chr].push(lodval);

-      }

-    }

-  }

-  if (lodvarname != null) {

-    data.markers = [];

-    _ref2 = data.markernames;

-    for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) {

-      marker = _ref2[i];

-      if (marker !== "") {

-        data.markers.push({

-          name: marker,

-          chr: data.chr[i],

-          pos: data.pos[i],

-          lod: data[lodvarname][i]

-        });

-      }

-    }

-  }

-  return data;

-};

-

-chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {

-  var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;

-  chrStart = [];

-  chrEnd = [];

-  chrLength = [];

-  totalChrLength = 0;

-  maxd = 0;

-  _ref = data.chrnames;

-  for (_i = 0, _len = _ref.length; _i < _len; _i++) {

-    chr = _ref[_i];

-    d = maxdiff(data.posByChr[chr]);

-    if (d > maxd) {

-      maxd = d;

-    }

-    rng = d3.extent(data.posByChr[chr]);

-    chrStart.push(rng[0]);

-    chrEnd.push(rng[1]);

-    L = rng[1] - rng[0];

-    chrLength.push(L);

-    totalChrLength += L;

-  }

-  if (pad4heatmap) {

-    data.recwidth = maxd;

-    chrStart = chrStart.map(function(x) {

-      return x - maxd / 2;

-    });

-    chrEnd = chrEnd.map(function(x) {

-      return x + maxd / 2;

-    });

-    chrLength = chrLength.map(function(x) {

-      return x + maxd;

-    });

-    totalChrLength += chrLength.length * maxd;

-  }

-  data.chrStart = [];

-  data.chrEnd = [];

-  cur = leftMargin;

-  if (!pad4heatmap) {

-    cur += chrGap / 2;

-  }

-  data.xscale = {};

-  _ref1 = data.chrnames;

-  for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) {

-    chr = _ref1[i];

-    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;

-    data.xscale[chr] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);

-  }

-  return data;

-};

-

-selectGroupColors = function(ngroup, palette) {

-  if (ngroup === 0) {

-    return [];

-  }

-  if (palette === "dark") {

-    if (ngroup === 1) {

-      return ["slateblue"];

-    }

-    if (ngroup === 2) {

-      return ["MediumVioletRed", "slateblue"];

-    }

-    if (ngroup <= 9) {

-      return colorbrewer.Set1[ngroup];

-    }

-    return d3.scale.category20().range().slice(0, ngroup);

-  } else {

-    if (ngroup === 1) {

-      return [d3.rgb(190, 190, 190)];

-    }

-    if (ngroup === 2) {

-      return ["lightpink", "lightblue"];

-    }

-    if (ngroup <= 9) {

-      return colorbrewer.Pastel1[ngroup];

-    }

-    return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"].slice(0, ngroup);

-  }

-};

-

-expand2vector = function(input, n) {

-  var i;

-  if (Array.isArray(input) && input.length >= n) {

-    return input;

-  }

-  if (!Array.isArray(input)) {

-    input = [input];

-  }

-  if (input.length === 1 && n > 1) {

-    input = (function() {

-      var _results;

-      _results = [];

-      for (i in d3.range(n)) {

-        _results.push(input[0]);

-      }

-      return _results;

-    })();

-  }

-  return input;

-};

-

-median = function(x) {

-  var n;

-  if (x == null) {

-    return null;

-  }

-  n = x.length;

-  x.sort(function(a, b) {

-    return a - b;

-  });

-  if (n % 2 === 1) {

-    return x[(n - 1) / 2];

-  }

-  return (x[n / 2] + x[(n / 2) - 1]) / 2;

-};

-

-getLeftRight = function(x) {

-  var i, n, result, v, xdif, _i, _j, _k, _len, _ref;

-  n = x.length;

-  x.sort(function(a, b) {

-    return a - b;

-  });

-  xdif = [];

-  result = {};

-  for (_i = 0, _len = x.length; _i < _len; _i++) {

-    v = x[_i];

-    result[v] = {};

-  }

-  for (i = _j = 1; 1 <= n ? _j < n : _j > n; i = 1 <= n ? ++_j : --_j) {

-    xdif.push(x[i] - x[i - 1]);

-    result[x[i]].left = x[i - 1];

-  }

-  for (i = _k = 0, _ref = n - 1; 0 <= _ref ? _k < _ref : _k > _ref; i = 0 <= _ref ? ++_k : --_k) {

-    result[x[i]].right = x[i + 1];

-  }

-  xdif = median(xdif);

-  result.mediandiff = xdif;

-  result[x[0]].left = x[0] - xdif;

-  result[x[n - 1]].right = x[n - 1] + xdif;

-  result.extent = [x[0] - xdif / 2, x[n - 1] + xdif / 2];

-  return result;

-};

-

-maxdiff = function(x) {

-  var d, i, result, _i, _ref;

-  if (x.length < 2) {

-    return null;

-  }

-  result = x[1] - x[0];

-  if (x.length < 3) {

-    return result;

-  }

-  for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) {

-    d = x[i] - x[i - 1];

-    if (d > result) {

-      result = d;

-    }

-  }

-  return result;

-};

-

-matrixMin = function(mat) {

-  var i, j, result;

-  result = mat[0][0];

-  for (i in mat) {

-    for (j in mat[i]) {

-      if (result > mat[i][j]) {

-        result = mat[i][j];

-      }

-    }

-  }

-  return result;

-};

-

-matrixMax = function(mat) {

-  var i, j, result;

-  result = mat[0][0];

-  for (i in mat) {

-    for (j in mat[i]) {

-      if (result < mat[i][j]) {

-        result = mat[i][j];

-      }

-    }

-  }

-  return result;

-};

-

-matrixMaxAbs = function(mat) {

-  var i, j, result;

-  result = Math.abs(mat[0][0]);

-  for (i in mat) {

-    for (j in mat[i]) {

-      if (result < mat[i][j]) {

-        result = Math.abs(mat[i][j]);

-      }

-    }

-  }

-  return result;

-};

-

-matrixExtent = function(mat) {

-  return [matrixMin(mat), matrixMax(mat)];

-};

-

-d3.selection.prototype.moveToFront = function() {

-  return this.each(function() {

-    return this.parentNode.appendChild(this);

-  });

-};

-

-d3.selection.prototype.moveToBack = function() {

-  return this.each(function() {

-    var firstChild;

-    firstChild = this.parentNode.firstchild;

-    if (firstChild) {

-      return this.parentNode.insertBefore(this, firstChild);

-    }

-  });

-};

-

-forceAsArray = function(x) {

-  if (Array.isArray(x)) {

-    return x;

-  }

-  return [x];

-};

+// Generated by CoffeeScript 1.7.1
+var abs, calc_crosstab, chrscales, colSums, displayError, expand2vector, forceAsArray, formatAxis, getLeftRight, log10, log2, matrixExtent, matrixMax, matrixMaxAbs, matrixMin, maxdiff, median, missing2null, pullVarAsArray, reorgLodData, rowSums, selectGroupColors, sumArray, transpose, unique;
+
+formatAxis = function(d, extra_digits) {
+  var ndig;
+  if (extra_digits == null) {
+    extra_digits = 0;
+  }
+  d = d[1] - d[0];
+  ndig = Math.floor(Math.log(d % 10) / Math.log(10));
+  if (ndig > 0) {
+    ndig = 0;
+  }
+  ndig = Math.abs(ndig) + extra_digits;
+  return d3.format("." + ndig + "f");
+};
+
+unique = function(x) {
+  var output, v, _i, _len, _results;
+  output = {};
+  for (_i = 0, _len = x.length; _i < _len; _i++) {
+    v = x[_i];
+    if (v) {
+      output[v] = v;
+    }
+  }
+  _results = [];
+  for (v in output) {
+    _results.push(output[v]);
+  }
+  return _results;
+};
+
+pullVarAsArray = function(data, variable) {
+  var i, v;
+  v = [];
+  for (i in data) {
+    v = v.concat(data[i][variable]);
+  }
+  return v;
+};
+
+reorgLodData = function(data, lodvarname) {
+  var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2;
+  if (lodvarname == null) {
+    lodvarname = null;
+  }
+  data.posByChr = {};
+  data.lodByChr = {};
+  _ref = data.chrnames;
+  for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
+    chr = _ref[i];
+    data.posByChr[chr[0]] = [];
+    data.lodByChr[chr[0]] = [];
+    _ref1 = data.pos;
+    for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {
+      pos = _ref1[j];
+      if (data.chr[j].toString() === chr[0]) {
+        data.posByChr[chr[0]].push(pos);
+        if (!Array.isArray(data.lodnames)) {
+          data.lodnames = [data.lodnames];
+        }
+        lodval = (function() {
+          var _k, _len2, _ref2, _results;
+          _ref2 = data.lodnames;
+          _results = [];
+          for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
+            lodcolumn = _ref2[_k];
+            _results.push(data[lodcolumn][j]);
+          }
+          return _results;
+        })();
+        data.lodByChr[chr[0]].push(lodval);
+      }
+    }
+  }
+  if (lodvarname != null) {
+    data.markers = [];
+    _ref2 = data.markernames;
+    for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) {
+      marker = _ref2[i];
+      if (marker !== "") {
+        data.markers.push({
+          name: marker,
+          chr: data.chr[i],
+          pos: data.pos[i],
+          lod: data[lodvarname][i]
+        });
+      }
+    }
+  }
+  return data;
+};
+
+chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
+  var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;
+  chrStart = [];
+  chrEnd = [];
+  chrLength = [];
+  totalChrLength = 0;
+  maxd = 0;
+  _ref = data.chrnames;
+  for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+    chr = _ref[_i];
+    d = maxdiff(data.posByChr[chr[0]]);
+    if (d > maxd) {
+      maxd = d;
+    }
+    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;
+  }
+  if (pad4heatmap) {
+    data.recwidth = maxd;
+    chrStart = chrStart.map(function(x) {
+      return x - maxd / 2;
+    });
+    chrEnd = chrEnd.map(function(x) {
+      return x + maxd / 2;
+    });
+    chrLength = chrLength.map(function(x) {
+      return x + maxd;
+    });
+    totalChrLength += chrLength.length * maxd;
+  }
+  data.chrStart = [];
+  data.chrEnd = [];
+  cur = leftMargin;
+  if (!pad4heatmap) {
+    cur += chrGap / 2;
+  }
+  data.xscale = {};
+  _ref1 = data.chrnames;
+  for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) {
+    chr = _ref1[i];
+    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;
+    data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
+  }
+  return data;
+};
+
+selectGroupColors = function(ngroup, palette) {
+  if (ngroup === 0) {
+    return [];
+  }
+  if (palette === "dark") {
+    if (ngroup === 1) {
+      return ["slateblue"];
+    }
+    if (ngroup === 2) {
+      return ["MediumVioletRed", "slateblue"];
+    }
+    if (ngroup <= 9) {
+      return colorbrewer.Set1[ngroup];
+    }
+    return d3.scale.category20().range().slice(0, ngroup);
+  } else {
+    if (ngroup === 1) {
+      return ["#bebebe"];
+    }
+    if (ngroup === 2) {
+      return ["lightpink", "lightblue"];
+    }
+    if (ngroup <= 9) {
+      return colorbrewer.Pastel1[ngroup];
+    }
+    return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"].slice(0, ngroup);
+  }
+};
+
+expand2vector = function(input, n) {
+  var i;
+  if (input == null) {
+    return input;
+  }
+  if (Array.isArray(input) && input.length >= n) {
+    return input;
+  }
+  if (!Array.isArray(input)) {
+    input = [input];
+  }
+  if (input.length === 1 && n > 1) {
+    input = (function() {
+      var _results;
+      _results = [];
+      for (i in d3.range(n)) {
+        _results.push(input[0]);
+      }
+      return _results;
+    })();
+  }
+  return input;
+};
+
+median = function(x) {
+  var n;
+  if (x == null) {
+    return null;
+  }
+  n = x.length;
+  x.sort(function(a, b) {
+    return a - b;
+  });
+  if (n % 2 === 1) {
+    return x[(n - 1) / 2];
+  }
+  return (x[n / 2] + x[(n / 2) - 1]) / 2;
+};
+
+getLeftRight = function(x) {
+  var i, n, result, v, xdif, _i, _j, _k, _len, _ref;
+  n = x.length;
+  x.sort(function(a, b) {
+    return a - b;
+  });
+  xdif = [];
+  result = {};
+  for (_i = 0, _len = x.length; _i < _len; _i++) {
+    v = x[_i];
+    result[v] = {};
+  }
+  for (i = _j = 1; 1 <= n ? _j < n : _j > n; i = 1 <= n ? ++_j : --_j) {
+    xdif.push(x[i] - x[i - 1]);
+    result[x[i]].left = x[i - 1];
+  }
+  for (i = _k = 0, _ref = n - 1; 0 <= _ref ? _k < _ref : _k > _ref; i = 0 <= _ref ? ++_k : --_k) {
+    result[x[i]].right = x[i + 1];
+  }
+  xdif = median(xdif);
+  result.mediandiff = xdif;
+  result[x[0]].left = x[0] - xdif;
+  result[x[n - 1]].right = x[n - 1] + xdif;
+  result.extent = [x[0] - xdif / 2, x[n - 1] + xdif / 2];
+  return result;
+};
+
+maxdiff = function(x) {
+  var d, i, result, _i, _ref;
+  if (x.length < 2) {
+    return null;
+  }
+  result = x[1] - x[0];
+  if (x.length < 3) {
+    return result;
+  }
+  for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) {
+    d = x[i] - x[i - 1];
+    if (d > result) {
+      result = d;
+    }
+  }
+  return result;
+};
+
+matrixMin = function(mat) {
+  var i, j, result;
+  result = mat[0][0];
+  for (i in mat) {
+    for (j in mat[i]) {
+      if (result > mat[i][j]) {
+        result = mat[i][j];
+      }
+    }
+  }
+  return result;
+};
+
+matrixMax = function(mat) {
+  var i, j, result;
+  result = mat[0][0];
+  for (i in mat) {
+    for (j in mat[i]) {
+      if (result < mat[i][j]) {
+        result = mat[i][j];
+      }
+    }
+  }
+  return result;
+};
+
+matrixMaxAbs = function(mat) {
+  var i, j, result;
+  result = Math.abs(mat[0][0]);
+  for (i in mat) {
+    for (j in mat[i]) {
+      if (result < mat[i][j]) {
+        result = Math.abs(mat[i][j]);
+      }
+    }
+  }
+  return result;
+};
+
+matrixExtent = function(mat) {
+  return [matrixMin(mat), matrixMax(mat)];
+};
+
+d3.selection.prototype.moveToFront = function() {
+  return this.each(function() {
+    return this.parentNode.appendChild(this);
+  });
+};
+
+d3.selection.prototype.moveToBack = function() {
+  return this.each(function() {
+    var firstChild;
+    firstChild = this.parentNode.firstchild;
+    if (firstChild) {
+      return this.parentNode.insertBefore(this, firstChild);
+    }
+  });
+};
+
+forceAsArray = function(x) {
+  if (x == null) {
+    return x;
+  }
+  if (Array.isArray(x)) {
+    return x;
+  }
+  return [x];
+};
+
+missing2null = function(vec, missingvalues) {
+  if (missingvalues == null) {
+    missingvalues = ['NA', ''];
+  }
+  return vec.map(function(value) {
+    if (missingvalues.indexOf(value) > -1) {
+      return null;
+    } else {
+      return value;
+    }
+  });
+};
+
+displayError = function(message) {
+  if (d3.select("div.error").empty()) {
+    d3.select("body").insert("div", ":first-child").attr("class", "error");
+  }
+  return d3.select("div.error").append("p").text(message);
+};
+
+sumArray = function(vec) {
+  return vec.reduce(function(a, b) {
+    return a + b;
+  });
+};
+
+calc_crosstab = function(data) {
+  var col, cs, i, ncol, nrow, result, row, rs, _i, _j;
+  nrow = data.ycat.length;
+  ncol = data.xcat.length;
+  result = (function() {
+    var _i, _results;
+    _results = [];
+    for (row = _i = 0; 0 <= nrow ? _i <= nrow : _i >= nrow; row = 0 <= nrow ? ++_i : --_i) {
+      _results.push((function() {
+        var _j, _results1;
+        _results1 = [];
+        for (col = _j = 0; 0 <= ncol ? _j <= ncol : _j >= ncol; col = 0 <= ncol ? ++_j : --_j) {
+          _results1.push(0);
+        }
+        return _results1;
+      })());
+    }
+    return _results;
+  })();
+  for (i in data.x) {
+    result[data.y[i]][data.x[i]] += 1;
+  }
+  rs = rowSums(result);
+  cs = colSums(result);
+  for (i = _i = 0; 0 <= ncol ? _i < ncol : _i > ncol; i = 0 <= ncol ? ++_i : --_i) {
+    result[nrow][i] = cs[i];
+  }
+  for (i = _j = 0; 0 <= nrow ? _j < nrow : _j > nrow; i = 0 <= nrow ? ++_j : --_j) {
+    result[i][ncol] = rs[i];
+  }
+  result[nrow][ncol] = sumArray(rs);
+  return result;
+};
+
+rowSums = function(mat) {
+  var x, _i, _len, _results;
+  _results = [];
+  for (_i = 0, _len = mat.length; _i < _len; _i++) {
+    x = mat[_i];
+    _results.push(sumArray(x));
+  }
+  return _results;
+};
+
+transpose = function(mat) {
+  var i, j, _i, _ref, _results;
+  _results = [];
+  for (j = _i = 0, _ref = mat[0].length; 0 <= _ref ? _i < _ref : _i > _ref; j = 0 <= _ref ? ++_i : --_i) {
+    _results.push((function() {
+      var _j, _ref1, _results1;
+      _results1 = [];
+      for (i = _j = 0, _ref1 = mat.length; 0 <= _ref1 ? _j < _ref1 : _j > _ref1; i = 0 <= _ref1 ? ++_j : --_j) {
+        _results1.push(mat[i][j]);
+      }
+      return _results1;
+    })());
+  }
+  return _results;
+};
+
+colSums = function(mat) {
+  return rowSums(transpose(mat));
+};
+
+log2 = function(x) {
+  if (x == null) {
+    return x;
+  }
+  return Math.log(x) / Math.log(2.0);
+};
+
+log10 = function(x) {
+  if (x == null) {
+    return x;
+  }
+  return Math.log(x) / Math.log(10.0);
+};
+
+abs = function(x) {
+  if (x == null) {
+    return x;
+  }
+  return Math.abs(x);
+};
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 27bf80d5..fc687c7a 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -170,6 +170,42 @@ $ ->
         #this.my_timer = setInterval(get_progress, 1000)
         #return false
     )
+    
+    $("#rqtl_geno_compute").click(() =>
+        $("#progress_bar_container").modal()
+        url = "/marker_regression"
+        $('input[name=method]').val("rqtl_geno")
+        $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val())
+        $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val())
+        form_data = $('#trait_data_form').serialize()
+        console.log("form_data is:", form_data)
+        
+        #remove_outliers = confirm("Remove outliers?")
+        #if use_outliers == true
+        #    block_outliers()
+        do_ajax_post(url, form_data)
+        
+        #$.ajax(
+        #    type: "POST"
+        #    url: url
+        #    data: form_data
+        #    error: (xhr, ajaxOptions, thrownError) =>
+        #        alert("Sorry, an error occurred")
+        #        console.log(xhr)
+        #        clearInterval(this.my_timer)
+        #        $('#progress_bar_container').modal('hide')
+        #        $("body").html("We got an error.")        
+        #    success: (data) =>
+        #        clearInterval(this.my_timer)
+        #        $('#progress_bar_container').modal('hide')
+        #        $("body").html(data)
+        #)
+        #console.log("settingInterval")
+        #
+        #this.my_timer = setInterval(get_progress, 1000)
+        #return false
+    )
+
 
     $("#plink_compute").click(() =>
         $("#static_progress_bar_container").modal()
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index d02bca4b..a8a42ffa 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -130,6 +130,19 @@ $(function() {
       return do_ajax_post(url, form_data);
     };
   })(this));
+  $("#rqtl_geno_compute").click((function(_this) {
+    return function() {
+      var form_data, url;
+      $("#progress_bar_container").modal();
+      url = "/marker_regression";
+      $('input[name=method]').val("rqtl_geno");
+      $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
+      $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
   $("#plink_compute").click((function(_this) {
     return function() {
       var form_data, url;
diff --git a/wqflask/wqflask/static/packages/DT_bootstrap/DT_bootstrap.js b/wqflask/wqflask/static/packages/DT_bootstrap/DT_bootstrap.js
index 328733f2..cfe3e9d2 100755
--- a/wqflask/wqflask/static/packages/DT_bootstrap/DT_bootstrap.js
+++ b/wqflask/wqflask/static/packages/DT_bootstrap/DT_bootstrap.js
@@ -148,12 +148,12 @@ if ( $.fn.DataTable.TableTools ) {
 
 
 /* Table initialisation */
-$(document).ready(function() {
-	$('#example').dataTable( {
-		"sDom": "<'row'<'span6'l><'span6'f>r>t<'row'<'span6'i><'span6'p>>",
-		"sPaginationType": "bootstrap",
-		"oLanguage": {
-			"sLengthMenu": "_MENU_ records per page"
-		}
-	} );
-} );
\ No newline at end of file
+//$(document).ready(function() {
+//	$('#example').dataTable( {
+//		"sDom": "<'row'<'span6'l><'span6'f>r>t<'row'<'span6'i><'span6'p>>",
+//		"sPaginationType": "bootstrap",
+//		"oLanguage": {
+//			"sLengthMenu": "_MENU_ records per page"
+//		}
+//	} );
+//} );
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 705eda88..c58b7729 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -9,6 +9,9 @@
                 <li>
                     <a href="#pylmm" data-toggle="tab">pyLMM</a>
                 </li>
+                <li>
+                    <a href="#rqtl_geno" data-toggle="tab">rqtl</a>
+                </li>
                 {% if dataset.group.species == 'human' %}
                 <li>
                     <a href="#plink" data-toggle="tab">PLINK</a>
@@ -49,7 +52,7 @@
                     <div class="control-group mapping_method_fields">
                         <label for="mapping_permutations" class="control-label">Permutations (n)</label>
                         <div class="controls">
-                            <input name="num_permutations" value="2000" type="text" />
+                            <input name="num_perm_reaper" value="2000" type="text" />
                         </div>
                     </div>
     
@@ -66,7 +69,7 @@
                         <div class="controls" id="display_additive_effect">                      
                             <label class="radio inline">
                                 <input type="radio" name="display_additive"
-                                       id="display_dditive" value="yes" checked>
+                                       id="display_additive" value="yes" checked>
                                 Yes
                             </label>
                             <label class="radio inline">
@@ -171,6 +174,33 @@
                     </div>
                     
                 </div>
+                <div class="tab-pane" id="rqtl_geno">
+                    
+                    <div class="control-group">
+                        <label for="num_perm_rqtl_geno" class="control-label">Permutations (n)</label>
+                        <div class="controls">
+                            <input name="num_perm_rqtl_geno" value="0" type="text" />
+                        </div>
+                    </div>
+                    <div class="control-group">
+                        <label for="control_rqtl_geno" class="control-label">Control Marker</label>
+                        <div class="controls">
+                            <input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" />
+                        </div>
+                    </div>
+                    
+                    <div class="control-group">
+                        <div class="controls">
+                            <button id="rqtl_geno_compute"
+                                    class="btn btn-inverse submit_special"
+                                    data-url="/marker_regression"
+                                    title="Compute Marker Regression">
+                                <i class="icon-ok-circle icon-white"></i> Compute
+                            </button>
+                        </div>
+                    </div>
+                    
+                </div>
                 
                 {% if dataset.group.species == 'human' %}
                 <div class="tab-pane" id="plink">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3c448988..26e690d4 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -209,7 +209,7 @@ def heatmap_page():
     start_vars = request.form
     temp_uuid = uuid.uuid4()
     
-    version = "v4"
+    version = "v5"
     key = "heatmap:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
     print("key is:", pf(key))
     with Bench("Loading cache"):
@@ -252,7 +252,10 @@ def marker_regression_page():
         'dataset',
         'method',
         'suggestive',
-        'maf'
+        'num_perm',
+        'maf',
+        'control_marker',
+        'control_marker_db'
     )
 
     start_vars = {}
@@ -260,7 +263,7 @@ def marker_regression_page():
         if key in wanted or key.startswith(('value:')):
             start_vars[key] = value
 
-    version = "v3"
+    version = "v4"
     key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
     print("key is:", pf(key))
     with Bench("Loading cache"):
@@ -296,7 +299,7 @@ def marker_regression_page():
         pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
         print("pickled result length:", len(pickled_result))
         Redis.set(key, pickled_result)
-        Redis.expire(key, 60*60)
+        Redis.expire(key, 1*60)
 
     with Bench("Rendering template"):
         rendered_template = render_template("marker_regression.html", **result)
@@ -346,7 +349,7 @@ def interval_mapping_page():
         if key in wanted or key.startswith(('value:')):
             start_vars[key] = value
 
-    version = "v11"
+    version = "v4"
     key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
     print("key is:", pf(key))
     with Bench("Loading cache"):