Made lines for manhattan plot proportional to chromosome lengths

6 files changed, 97 insertions, 48 deletions

diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 920d9ac6..d2567b63 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -2,14 +2,16 @@ from __future__ import absolute_import, print_function, division
 
 from base.trait import GeneralTrait
 from base import data_set
+from base.species import TheSpecies
 
-def get_dataset_and_trait(self, start_vars):
+def get_species_dataset_trait(self, start_vars):
     #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
     self.dataset = data_set.create_dataset(start_vars['dataset'])
+    self.species = TheSpecies(dataset=self.dataset)
     self.this_trait = GeneralTrait(dataset=self.dataset.name,
                                    name=start_vars['trait_id'],
                                    cellid=None)
     
     #if read_genotype:
     self.dataset.group.read_genotype_file()
-    self.genotype = self.dataset.group.genotype    
\ No newline at end of file
+    self.genotype = self.dataset.group.genotype
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 81bf3825..50739614 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -24,6 +24,7 @@ from utility import Plot, Bunch
 from wqflask.interval_analyst import GeneUtil
 from base.trait import GeneralTrait
 from base import data_set
+from base import species
 from base.templatePage import templatePage
 from utility import webqtlUtil, helper_functions
 from base import webqtlConfig
@@ -60,7 +61,7 @@ class MarkerRegression(object):
 
         #print("start_vars are: ", pf(start_vars))
 
-        helper_functions.get_dataset_and_trait(self, start_vars)
+        helper_functions.get_species_dataset_trait(self, start_vars)
 
         self.num_perm = int(start_vars['num_perm'])
 
@@ -306,7 +307,14 @@ class MarkerRegression(object):
 
             # end: common part with human data
             
+            chromosome_mb_lengths = {}
+            for key in self.species.chromosomes.chromosomes.keys():
+                chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
+            
+            print("chromosomes is:", pf(chromosome_mb_lengths))
+            
             self.js_data = dict(
+                chromosomes = chromosome_mb_lengths,
                 qtl_results = self.pure_qtl_results,
                 lrs_values = self.lrs_values,
             )
@@ -476,25 +484,24 @@ class MarkerRegression(object):
         #prep_data.PrepData(self.vals, genotype_data)
         
         pheno_vector = np.array([float(val) for val in self.vals if val!="x"])
-        print("genotypes was:", pf(trimmed_genotype_data))
-        for item in trimmed_genotype_data:
-            if type(item) != type(list()):
-                print(" --->", type(item))
-            for counter, part in enumerate(item):
-                if type(part) != type(float()):
-                    print(" ------>", type(part), " : ", part)
-                if counter % 100 == 0:
-                    print(" ------>", type(part))
+        #for item in trimmed_genotype_data:
+        #    if type(item) != type(list()):
+        #        print(" --->", type(item))
+        #    for counter, part in enumerate(item):
+        #        if type(part) != type(float()):
+        #            print(" ------>", type(part), " : ", part)
+        #        if counter % 100 == 0:
+        #            print(" ------>", type(part))
         genotypes = np.array(trimmed_genotype_data).T
-        print("genotypes is:", pf(genotypes))
+        #print("genotypes is:", pf(genotypes))
         #genotypes = np.genfromtxt(os.path.join(webqtlConfig.TMPDIR,
         #                                       self.dataset.group.name + '.snps.new')).T
         
-        print("pheno_vector is:", pf(pheno_vector.shape))
-        print("genotypes is:", pf(genotypes.shape))
+        #print("pheno_vector is:", pf(pheno_vector.shape))
+        #print("genotypes is:", pf(genotypes.shape))
         
         kinship_matrix = lmm.calculateKinship(genotypes)
-        print("kinship_matrix is:", pf(kinship_matrix))
+        #print("kinship_matrix is:", pf(kinship_matrix))
         
         lmm_ob = lmm.LMM(pheno_vector, kinship_matrix)
         lmm_ob.fit()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 33ea6e86..720515c1 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -38,7 +38,7 @@ class ShowTrait(object):
         print("in ShowTrait, kw are:", kw)
         self.trait_id = kw['trait_id']
         
-        helper_functions.get_dataset_and_trait(self, kw)
+        helper_functions.get_species_dataset_trait(self, kw)
 
         #self.dataset = create_dataset(kw['dataset'])
         #
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 41632723..6bdb3ac6 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -4,7 +4,9 @@ $ ->
 
         constructor: ->
             @qtl_results = js_data.qtl_results
+            @chromosomes = js_data.chromosomes
             @max_chr = @get_max_chr()
+            @cumulative_chr_lengths = @get_cumulative_chr_lengths()
 
             @plot_height = 500
             @plot_width = 1000
@@ -31,9 +33,22 @@ $ ->
                         max_chr = chr
             return max_chr
 
+        get_cumulative_chr_lengths: () ->
+            cumulative_chr_lengths = []
+            total_length = 0
+            for key of @chromosomes
+                this_length = @chromosomes[key]
+                cumulative_chr_lengths.push(total_length + this_length)
+                total_length += this_length
+            console.log("lengths:", cumulative_chr_lengths)
+            return cumulative_chr_lengths
+
 
         get_coordinates: () ->
+            total_length = 0
+            chr_lengths = []
             for result in js_data.qtl_results
+                chr_length = @chromosomes[result.chr]
                 chr = parseInt(result.chr)
                 if _.isNaN(chr)
                     if result.chr == "X"
@@ -41,9 +56,17 @@ $ ->
                     else if result.chr == "Y"
                         chr = @max_chr + 2
         
-                @x_coords.push(((chr-1) * 200) + parseFloat(result.Mb))
+                @x_coords.push(total_length + parseFloat(result.Mb))
                 @y_coords.push(result.lrs_value)
                 @marker_names.push(result.name)
+                
+                if chr_length in chr_lengths
+                    continue
+                else
+                    chr_lengths.push(chr_length)
+                    total_length += chr_length
+
+            console.log("chr_lengths are:", @chr_lengths)
 
 
         display_info: (d) ->
@@ -56,20 +79,20 @@ $ ->
                         .attr("width", @plot_width)
                         .attr("height", @plot_height)
         
-            svg.selectAll("text")
-                .data(@plot_coordinates)
-                .enter()
-                .append("text")
-                .attr("x", (d) =>
-                    return (@plot_width * d[0]/@x_max)
-                )
-                .attr("y", (d) =>
-                    return @plot_height - ((0.8*@plot_height) * d[1]/@y_max)
-                )
-                .text((d) => d[2])
-                .attr("font-family", "sans-serif")
-                .attr("font-size", "12px")
-                .attr("fill", "black");
+            #svg.selectAll("text")
+            #    .data(@plot_coordinates)
+            #    .enter()
+            #    .append("text")
+            #    .attr("x", (d) =>
+            #        return (@plot_width * d[0]/@x_max)
+            #    )
+            #    .attr("y", (d) =>
+            #        return @plot_height - ((0.8*@plot_height) * d[1]/@y_max)
+            #    )
+            #    .text((d) => d[2])
+            #    .attr("font-family", "sans-serif")
+            #    .attr("font-size", "12px")
+            #    .attr("fill", "black");
             
             svg.selectAll("circle")
                 .data(@plot_coordinates)
@@ -116,7 +139,7 @@ $ ->
                 )
                 .on("mouseout", () =>
                     d3.select(d3.event.target).classed("d3_highlight", false)
-                        .attr("r", 2)
+                       .attr("r", 2)
                         .attr("fill", "black")
                 )
                 .attr("title", "foobar")
@@ -132,7 +155,7 @@ $ ->
                 .range([0, @plot_height])
                 
             svg.selectAll("line")
-                .data(x.ticks(@max_chr))
+                .data(@cumulative_chr_lengths)
                 .enter()
                 .append("line")
                 .attr("x1", x)
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index 68e04034..19fec21e 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -1,5 +1,6 @@
 // Generated by CoffeeScript 1.3.3
 (function() {
+  var __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
 
   $(function() {
     var Manhattan_Plot;
@@ -7,7 +8,9 @@
 
       function Manhattan_Plot() {
         this.qtl_results = js_data.qtl_results;
+        this.chromosomes = js_data.chromosomes;
         this.max_chr = this.get_max_chr();
+        this.cumulative_chr_lengths = this.get_cumulative_chr_lengths();
         this.plot_height = 500;
         this.plot_width = 1000;
         this.x_coords = [];
@@ -37,12 +40,27 @@
         return max_chr;
       };
 
+      Manhattan_Plot.prototype.get_cumulative_chr_lengths = function() {
+        var cumulative_chr_lengths, key, this_length, total_length;
+        cumulative_chr_lengths = [];
+        total_length = 0;
+        for (key in this.chromosomes) {
+          this_length = this.chromosomes[key];
+          cumulative_chr_lengths.push(total_length + this_length);
+          total_length += this_length;
+        }
+        console.log("lengths:", cumulative_chr_lengths);
+        return cumulative_chr_lengths;
+      };
+
       Manhattan_Plot.prototype.get_coordinates = function() {
-        var chr, result, _i, _len, _ref, _results;
+        var chr, chr_length, chr_lengths, result, total_length, _i, _len, _ref;
+        total_length = 0;
+        chr_lengths = [];
         _ref = js_data.qtl_results;
-        _results = [];
         for (_i = 0, _len = _ref.length; _i < _len; _i++) {
           result = _ref[_i];
+          chr_length = this.chromosomes[result.chr];
           chr = parseInt(result.chr);
           if (_.isNaN(chr)) {
             if (result.chr === "X") {
@@ -51,11 +69,17 @@
               chr = this.max_chr + 2;
             }
           }
-          this.x_coords.push(((chr - 1) * 200) + parseFloat(result.Mb));
+          this.x_coords.push(total_length + parseFloat(result.Mb));
           this.y_coords.push(result.lrs_value);
-          _results.push(this.marker_names.push(result.name));
+          this.marker_names.push(result.name);
+          if (__indexOf.call(chr_lengths, chr_length) >= 0) {
+            continue;
+          } else {
+            chr_lengths.push(chr_length);
+            total_length += chr_length;
+          }
         }
-        return _results;
+        return console.log("chr_lengths are:", this.chr_lengths);
       };
 
       Manhattan_Plot.prototype.display_info = function(d) {
@@ -66,13 +90,6 @@
         var svg, x, y,
           _this = this;
         svg = d3.select("#manhattan_plots").append("svg").style('border', '2px solid black').attr("width", this.plot_width).attr("height", this.plot_height);
-        svg.selectAll("text").data(this.plot_coordinates).enter().append("text").attr("x", function(d) {
-          return _this.plot_width * d[0] / _this.x_max;
-        }).attr("y", function(d) {
-          return _this.plot_height - ((0.8 * _this.plot_height) * d[1] / _this.y_max);
-        }).text(function(d) {
-          return d[2];
-        }).attr("font-family", "sans-serif").attr("font-size", "12px").attr("fill", "black");
         svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) {
           return _this.plot_width * d[0] / _this.x_max;
         }).attr("cy", function(d) {
@@ -84,7 +101,7 @@
         }).attr("title", "foobar");
         x = d3.scale.linear().domain([0, this.x_max]).range([0, this.plot_width]);
         y = d3.scale.linear().domain([0, this.y_max]).range([0, this.plot_height]);
-        return svg.selectAll("line").data(x.ticks(this.max_chr)).enter().append("line").attr("x1", x).attr("x2", x).attr("y1", 0).attr("y2", this.plot_height).style("stroke", "#ccc");
+        return svg.selectAll("line").data(this.cumulative_chr_lengths).enter().append("line").attr("x1", x).attr("x2", x).attr("y1", 0).attr("y2", this.plot_height).style("stroke", "#ccc");
       };
 
       return Manhattan_Plot;
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 81777742..5f2df8a4 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -154,7 +154,7 @@ def marker_regression_page():
     template_vars.js_data = json.dumps(template_vars.js_data,
                                        default=json_default_handler,
                                        indent="   ")
-    print("[dub] js_data after dump:", template_vars.js_data)
+    #print("[dub] js_data after dump:", template_vars.js_data)
     #print("marker_regression template_vars:", pf(template_vars.__dict__))
     return render_template("marker_regression.html", **template_vars.__dict__)