-
-
+
+
+
-
+
+
+
--
cgit v1.2.3
From 17ed5f2a56e03ded169b3191a7a7d280c5b584bf Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 12 Dec 2013 00:19:05 +0000
Subject: Put the code that rebuilds the bar chart into a function
Still need to fix issue where attribute colors don't stay with
their associated samples/strains
---
.../wqflask/static/new/javascript/bar_chart.coffee | 172 +++++++++++++--------
wqflask/wqflask/static/new/javascript/bar_chart.js | 108 +++++++------
2 files changed, 160 insertions(+), 120 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
index f59d947d..e1bb36e1 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
@@ -2,6 +2,7 @@ root = exports ? this
class Bar_Chart
constructor: (@sample_list, @sample_group) ->
+ @sort_by = "name"
@get_samples()
console.log("sample names:", @sample_names)
if @sample_attr_vals.length > 0
@@ -28,18 +29,19 @@ class Bar_Chart
@create_graph()
d3.select("#color_attribute").on("change", =>
- attribute = $("#color_attribute").val()
+ @attribute = $("#color_attribute").val()
console.log("attr_color_dict:", @attr_color_dict)
- if $("#update_bar_chart").html() == 'Sort By Name'
+ #if $("#update_bar_chart").html() == 'Sort By Name'
+ if @sort_by = "name"
@svg.selectAll(".bar")
.data(@sorted_samples())
.transition()
.duration(1000)
.style("fill", (d) =>
- if attribute == "None"
+ if @attribute == "None"
return "steelblue"
else
- return @attr_color_dict[attribute][d[2][attribute]]
+ return @attr_color_dict[@attribute][d[2][@attribute]]
)
.select("title")
.text((d) =>
@@ -51,79 +53,85 @@ class Bar_Chart
.transition()
.duration(1000)
.style("fill", (d) =>
- if attribute == "None"
+ if @attribute == "None"
return "steelblue"
else
- return @attr_color_dict[attribute][d[2][attribute]]
+ return @attr_color_dict[@attribute][d[2][@attribute]]
)
- @add_legend(attribute, @distinct_attr_vals[attribute])
+ @add_legend(@attribute, @distinct_attr_vals[@attribute])
)
-
-
-
+
$(".sort_by_value").on("click", =>
console.log("sorting by value")
- sortItems = (a, b) ->
- return a[1] - b[1]
-
- @svg.selectAll(".bar")
- .data(@sorted_samples())
- .transition()
- .duration(1000)
- .attr("y", (d) =>
- return @y_scale(d[1])
- )
- .attr("height", (d) =>
- return @plot_height - @y_scale(d[1])
- )
- .style("fill", (d) =>
- if @attributes.length > 0
- return @attr_color_dict[attribute][d[2][attribute]]
- else
- return "steelblue"
- )
- .select("title")
- .text((d) =>
- return d[1]
- )
- sorted_sample_names = (sample[0] for sample in @sorted_samples())
- x_scale = d3.scale.ordinal()
- .domain(sorted_sample_names)
- .rangeBands([0, @plot_width], .1)
- $('.x.axis').remove()
- @add_x_axis(x_scale)
+ @sort_by = "value"
+ if @attributes.length > 0
+ @attribute = $("#color_attribute").val()
+ #sortItems = (a, b) ->
+ # return a[1] - b[1]
+ @rebuild_bar_graph(@sorted_samples())
+ #@svg.selectAll(".bar")
+ # .data(@sorted_samples())
+ # .transition()
+ # .duration(1000)
+ # .attr("y", (d) =>
+ # return @y_scale(d[1])
+ # )
+ # .attr("height", (d) =>
+ # return @plot_height - @y_scale(d[1])
+ # )
+ # .select("title")
+ # .text((d) =>
+ # return d[1]
+ # )
+ # #.style("fill", (d) =>
+ # # if @attributes.length > 0
+ # # return @attr_color_dict[attribute][d[2][attribute]]
+ # # else
+ # # return "steelblue"
+ # #)
+ #sorted_sample_names = (sample[0] for sample in @sorted_samples())
+ #x_scale = d3.scale.ordinal()
+ # .domain(sorted_sample_names)
+ # .rangeBands([0, @plot_width], .1)
+ #$('.x.axis').remove()
+ #@add_x_axis(x_scale)
)
$(".sort_by_name").on("click", =>
console.log("sorting by name")
- #$("#update_bar_chart").html('Sort By Value')
- @svg.selectAll(".bar")
- .data(@samples)
- .transition()
- .duration(1000)
- .attr("y", (d) =>
- return @y_scale(d[1])
- )
- .attr("height", (d) =>
- return @plot_height - @y_scale(d[1])
- )
- .style("fill", (d) =>
- if @attributes.length > 0
- return @attr_color_dict[attribute][d[2][attribute]]
- else
- return "steelblue"
- )
- .select("title")
- .text((d) =>
- return d[1]
- )
- x_scale = d3.scale.ordinal()
- .domain(@sample_names)
- .rangeBands([0, @plot_width], .1)
- $('.x.axis').remove()
- @add_x_axis(x_scale)
+ @sort_by = "name"
+ if @attributes.length > 0
+ @attribute = $("#color_attribute").val()
+ @rebuild_bar_graph(@samples)
+ #@svg.selectAll(".bar")
+ # .data(@samples)
+ # .transition()
+ # .duration(1000)
+ # .attr("y", (d) =>
+ # return @y_scale(d[1])
+ # )
+ # .attr("height", (d) =>
+ # return @plot_height - @y_scale(d[1])
+ # )
+ # .select("title")
+ # .text((d) =>
+ # return d[1]
+ # )
+ # .style("fill", (d) =>
+ # if @attributes.length > 0
+ # return @attr_color_dict[attribute][d[2][attribute]]
+ # else
+ # return "steelblue"
+ # )
+ #x_scale = d3.scale.ordinal()
+ # .domain(@sample_names)
+ # .rangeBands([0, @plot_width], .1)
+ #$('.x.axis').remove()
+ #@add_x_axis(x_scale)
)
+
+
#d3.select(".update_bar_chart").on("click", =>
# console.log("THIS IS:", $(this))
# sort_by = $(this).val()
@@ -197,6 +205,40 @@ class Bar_Chart
)
+
+ rebuild_bar_graph: (samples) ->
+ console.log("samples:", samples)
+ @svg.selectAll(".bar")
+ .data(samples)
+ .transition()
+ .duration(1000)
+ .attr("y", (d) =>
+ return @y_scale(d[1])
+ )
+ .attr("height", (d) =>
+ return @plot_height - @y_scale(d[1])
+ )
+ .select("title")
+ .text((d) =>
+ return d[1]
+ )
+ .style("fill", (d) =>
+ if @attributes.length > 0 and @attribute != "None"
+ console.log("@attribute:", @attribute)
+ console.log("d[2]", d[2])
+ console.log("the_color:", @attr_color_dict[@attribute][d[2][@attribute]])
+ return @attr_color_dict[@attribute][d[2][@attribute]]
+ else
+ return "steelblue"
+ )
+ sample_names = (sample[0] for sample in samples)
+ console.log("sample_names2:", sample_names)
+ x_scale = d3.scale.ordinal()
+ .domain(sample_names)
+ .rangeBands([0, @plot_width], .1)
+ $('.x.axis').remove()
+ @add_x_axis(x_scale)
+
get_attr_color_dict: (vals) ->
@attr_color_dict = {}
console.log("vals:", vals)
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js
index 63a71857..b02ee1da 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.js
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.js
@@ -13,6 +13,7 @@
_this = this;
this.sample_list = sample_list;
this.sample_group = sample_group;
+ this.sort_by = "name";
this.get_samples();
console.log("sample names:", this.sample_names);
if (this.sample_attr_vals.length > 0) {
@@ -46,88 +47,85 @@
this.create_scales();
this.create_graph();
d3.select("#color_attribute").on("change", function() {
- var attribute;
- attribute = $("#color_attribute").val();
+ _this.attribute = $("#color_attribute").val();
console.log("attr_color_dict:", _this.attr_color_dict);
- if ($("#update_bar_chart").html() === 'Sort By Name') {
+ if (_this.sort_by = "name") {
_this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).style("fill", function(d) {
- if (attribute === "None") {
+ if (_this.attribute === "None") {
return "steelblue";
} else {
- return _this.attr_color_dict[attribute][d[2][attribute]];
+ return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]];
}
}).select("title").text(function(d) {
return d[1];
});
} else {
_this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).style("fill", function(d) {
- if (attribute === "None") {
+ if (_this.attribute === "None") {
return "steelblue";
} else {
- return _this.attr_color_dict[attribute][d[2][attribute]];
+ return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]];
}
});
}
- return _this.add_legend(attribute, _this.distinct_attr_vals[attribute]);
+ return _this.add_legend(_this.attribute, _this.distinct_attr_vals[_this.attribute]);
});
$(".sort_by_value").on("click", function() {
- var sortItems, sorted_sample_names, x_scale;
console.log("sorting by value");
- sortItems = function(a, b) {
- return a[1] - b[1];
- };
- _this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).attr("y", function(d) {
- return _this.y_scale(d[1]);
- }).attr("height", function(d) {
- return _this.plot_height - _this.y_scale(d[1]);
- }).style("fill", function(d) {
- if (_this.attributes.length > 0) {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- } else {
- return "steelblue";
- }
- }).select("title").text(function(d) {
- return d[1];
- });
- sorted_sample_names = (function() {
- var _i, _len, _ref, _results;
- _ref = this.sorted_samples();
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- _results.push(sample[0]);
- }
- return _results;
- }).call(_this);
- x_scale = d3.scale.ordinal().domain(sorted_sample_names).rangeBands([0, _this.plot_width], .1);
- $('.x.axis').remove();
- return _this.add_x_axis(x_scale);
+ _this.sort_by = "value";
+ if (_this.attributes.length > 0) {
+ _this.attribute = $("#color_attribute").val();
+ }
+ return _this.rebuild_bar_graph(_this.sorted_samples());
});
$(".sort_by_name").on("click", function() {
- var x_scale;
console.log("sorting by name");
- _this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).attr("y", function(d) {
- return _this.y_scale(d[1]);
- }).attr("height", function(d) {
- return _this.plot_height - _this.y_scale(d[1]);
- }).style("fill", function(d) {
- if (_this.attributes.length > 0) {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- } else {
- return "steelblue";
- }
- }).select("title").text(function(d) {
- return d[1];
- });
- x_scale = d3.scale.ordinal().domain(_this.sample_names).rangeBands([0, _this.plot_width], .1);
- $('.x.axis').remove();
- return _this.add_x_axis(x_scale);
+ _this.sort_by = "name";
+ if (_this.attributes.length > 0) {
+ _this.attribute = $("#color_attribute").val();
+ }
+ return _this.rebuild_bar_graph(_this.samples);
});
d3.select("#color_by_trait").on("click", function() {
return _this.open_trait_selection();
});
}
+ Bar_Chart.prototype.rebuild_bar_graph = function(samples) {
+ var sample, sample_names, x_scale,
+ _this = this;
+ console.log("samples:", samples);
+ this.svg.selectAll(".bar").data(samples).transition().duration(1000).attr("y", function(d) {
+ return _this.y_scale(d[1]);
+ }).attr("height", function(d) {
+ return _this.plot_height - _this.y_scale(d[1]);
+ }).select("title").text(function(d) {
+ return d[1];
+ }).style("fill", function(d) {
+ if (_this.attributes.length > 0 && _this.attribute !== "None") {
+ console.log("@attribute:", _this.attribute);
+ console.log("d[2]", d[2]);
+ console.log("the_color:", _this.attr_color_dict[_this.attribute][d[2][_this.attribute]]);
+ return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]];
+ } else {
+ return "steelblue";
+ }
+ });
+ sample_names = (function() {
+ var _i, _len, _results;
+ _results = [];
+ for (_i = 0, _len = samples.length; _i < _len; _i++) {
+ sample = samples[_i];
+ _results.push(sample[0]);
+ }
+ return _results;
+ })();
+ console.log("sample_names2:", sample_names);
+ x_scale = d3.scale.ordinal().domain(sample_names).rangeBands([0, this.plot_width], .1);
+ $('.x.axis').remove();
+ return this.add_x_axis(x_scale);
+ };
+
Bar_Chart.prototype.get_attr_color_dict = function(vals) {
var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _results,
_this = this;
--
cgit v1.2.3
From b73346af1c423103625545168271af7f1389623f Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Tue, 17 Dec 2013 23:29:38 +0000
Subject: Added the option to choose which method to use for the interval
mapping function (pyLMM or qtl reaper)
---
.../wqflask/interval_mapping/interval_mapping.py | 97 +++++++++++++++-------
.../wqflask/marker_regression/marker_regression.py | 1 -
.../static/new/javascript/interval_mapping.coffee | 57 ++++++-------
.../static/new/javascript/interval_mapping.js | 21 ++---
.../static/new/javascript/marker_regression.coffee | 8 +-
.../static/new/javascript/marker_regression.js | 7 +-
.../new/javascript/show_trait_mapping_tools.coffee | 5 ++
.../new/javascript/show_trait_mapping_tools.js | 7 +-
wqflask/wqflask/templates/base.html | 2 +-
wqflask/wqflask/templates/interval_mapping.html | 15 ++--
wqflask/wqflask/templates/show_trait.html | 4 +-
.../templates/show_trait_mapping_tools.html | 16 +++-
wqflask/wqflask/views.py | 1 +
13 files changed, 153 insertions(+), 88 deletions(-)
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index de7a2704..f0985cc2 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -37,8 +37,6 @@ class IntervalMapping(object):
def __init__(self, start_vars, temp_uuid):
- print("TESTING!!!")
-
#Currently only getting trait data for one trait, but will need
#to change this to accept multiple traits once the collection page is implemented
helper_functions.get_species_dataset_trait(self, start_vars)
@@ -57,7 +55,11 @@ class IntervalMapping(object):
self.set_options(start_vars)
- self.gen_qtl_results(tempdata)
+ if self.method == "qtl_reaper":
+ self.gen_reaper_results(tempdata)
+ else:
+ self.gen_pylmm_results(tempdata)
+ #self.gen_qtl_results(tempdata)
#Get chromosome lengths for drawing the interval map plot
chromosome_mb_lengths = {}
@@ -78,6 +80,7 @@ class IntervalMapping(object):
#self.plot_scale = start_vars['scale']
#if self.plotScale == 'physic' and not fd.genotype.Mbmap:
# self.plotScale = 'morgan'
+ self.method = start_vars['mapping_method']
self.num_permutations = int(start_vars['num_permutations'])
#self.do_bootstrap = start_vars['do_bootstrap']
self.selected_chr = start_vars['chromosome']
@@ -125,9 +128,6 @@ class IntervalMapping(object):
# variance = variances,
# control = self.control_locus)
#else:
- #reaper_results = self.dataset.group.genotype.regression(strains = trimmed_samples,
- # trait = trimmed_values,
- # control = self.control_locus)
reaper_results = genotype.regression(strains = trimmed_samples,
trait = trimmed_values,
control = self.control_locus)
@@ -139,8 +139,6 @@ class IntervalMapping(object):
#else:
print("strains:", trimmed_samples)
print("trait:", trimmed_values)
- #reaper_results = self.dataset.group.genotype.regression(strains = trimmed_samples,
- # trait = trimmed_values)
reaper_results = genotype.regression(strains = trimmed_samples,
trait = trimmed_values)
@@ -152,29 +150,70 @@ class IntervalMapping(object):
qtl = {"lrs": qtl.lrs, "locus": locus, "additive": qtl.additive}
self.qtl_results.append(qtl)
- #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
- #if self.dataset.group.species == "human":
- # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
- #else:
- #genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
- #
- #no_val_samples = self.identify_empty_samples()
- #trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
- #
- #genotype_matrix = np.array(trimmed_genotype_data).T
-
- #t_stats, p_values = lmm.run(
- # pheno_vector,
- # genotype_matrix,
- # restricted_max_likelihood=True,
- # refit=False,
- # temp_data=tempdata
- #)
-
- #self.dataset.group.markers.add_pvalues(p_values)
+ def gen_reaper_results(self, tempdata):
+ genotype = self.dataset.group.read_genotype_file()
+
+ samples, values, variances = self.this_trait.export_informative()
+
+ trimmed_samples = []
+ trimmed_values = []
+ for i in range(0, len(samples)):
+ if samples[i] in self.dataset.group.samplelist:
+ trimmed_samples.append(samples[i])
+ trimmed_values.append(values[i])
+
+ self.lrs_array = genotype.permutation(strains = trimmed_samples,
+ trait = trimmed_values,
+ nperm= self.num_permutations)
+ self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)]
+ self.significant = self.lrs_array[int(self.num_permutations*0.95-1)]
+
+ print("samples:", trimmed_samples)
+
+ if self.control_locus:
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values,
+ control = self.control_locus)
+ else:
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values)
+
+ #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+ self.qtl_results = []
+ for qtl in reaper_results:
+ reaper_locus = qtl.locus
+ locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
+ qtl = {"lrs_value": qtl.lrs, "chr":reaper_locus.chr, "Mb":reaper_locus.Mb,
+ "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive}
+ self.qtl_results.append(qtl)
+
+ def gen_pylmm_results(self, tempdata):
+ print("USING PYLMM")
+ self.dataset.group.get_markers()
- #self.qtl_results = self.dataset.group.markers.markers
+ pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
+ if self.dataset.group.species == "human":
+ p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
+ else:
+ genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
+
+ no_val_samples = self.identify_empty_samples()
+ trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
+
+ genotype_matrix = np.array(trimmed_genotype_data).T
+
+ t_stats, p_values = lmm.run(
+ pheno_vector,
+ genotype_matrix,
+ restricted_max_likelihood=True,
+ refit=False,
+ temp_data=tempdata
+ )
+
+ print("p_values:", p_values)
+ self.dataset.group.markers.add_pvalues(p_values)
+ self.qtl_results = self.dataset.group.markers.markers
def gen_qtl_results_2(self, tempdata):
"""Generates qtl results for plotting interval map"""
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 334ce631..006c586b 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -91,7 +91,6 @@ class MarkerRegression(object):
)
self.dataset.group.markers.add_pvalues(p_values)
-
self.qtl_results = self.dataset.group.markers.markers
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
index 0aa21d97..81db186b 100644
--- a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
@@ -66,30 +66,30 @@ $ ->
chr_lengths.push(this_length)
cumulative_chr_lengths.push(total_length + this_length)
total_length += this_length
-
+
console.log("chr_lengths: ", chr_lengths)
-
+
return [chr_lengths, cumulative_chr_lengths]
-
+
create_coordinates: () ->
chr_lengths = []
chr_seen = []
for result in js_data.qtl_results
- if result.locus.chr == "X"
+ if result.chr == "X"
chr_length = parseFloat(@chromosomes[20])
else
- chr_length = parseFloat(@chromosomes[result.locus.chr])
- if not(result.locus.chr in chr_seen)
- chr_seen.push(result.locus.chr)
+ chr_length = parseFloat(@chromosomes[result.chr])
+ if not(result.chr in chr_seen)
+ chr_seen.push(result.chr)
chr_lengths.push(chr_length)
- if result.locus.chr != "1"
+ if result.chr != "1"
@total_length += parseFloat(chr_lengths[chr_lengths.length - 2])
- @x_coords.push(@total_length + parseFloat(result.locus.Mb))
- @y_coords.push(result.lrs)
- @marker_names.push(result.locus.name)
+ @x_coords.push(@total_length + parseFloat(result.Mb))
+ @y_coords.push(result.lrs_value)
+ @marker_names.push(result.name)
@total_length += parseFloat(chr_lengths[chr_lengths.length-1])
#console.log("chr_lengths: ", chr_lengths)
-
+
create_svg: () ->
svg = d3.select("#interval_map")
.append("svg")
@@ -98,7 +98,7 @@ $ ->
.attr("height", @plot_height+@y_buffer)
return svg
-
+
create_graph: () ->
@add_border()
@add_x_axis()
@@ -107,13 +107,13 @@ $ ->
@fill_chr_areas()
@add_chr_labels()
@connect_markers()
-
+
add_border: () ->
border_coords = [[@y_buffer, @plot_height, @x_buffer, @x_buffer],
[@y_buffer, @plot_height, @plot_width, @plot_width],
[@y_buffer, @y_buffer, @x_buffer, @plot_width],
[@plot_height, @plot_height, @x_buffer, @plot_width]]
-
+
@svg.selectAll("line")
.data(border_coords)
.enter()
@@ -131,16 +131,16 @@ $ ->
return d[3]
)
.style("stroke", "#000")
-
+
create_scales: () ->
@x_scale = d3.scale.linear()
.domain([0, d3.max(@x_coords)])
.range([@x_buffer, @plot_width])
-
+
@y_scale = d3.scale.linear()
.domain([0, @y_max])
.range([@plot_height, @y_buffer])
-
+
create_x_axis_tick_values: () ->
tick_vals = []
for val in [25..@cumulative_chr_lengths[0]] when val%25 == 0
@@ -159,13 +159,13 @@ $ ->
#console.log("tick_vals:", tick_vals)
return tick_vals
-
+
add_x_axis: () ->
xAxis = d3.svg.axis()
.scale(@x_scale)
.orient("bottom")
.tickValues(@create_x_axis_tick_values())
-
+
next_chr = 1
tmp_tick_val = 0
xAxis.tickFormat((d) =>
@@ -183,7 +183,7 @@ $ ->
tick_val = tmp_tick_val
return (tick_val)
)
-
+
@svg.append("g")
.attr("class", "x_axis")
.attr("transform", "translate(0," + @plot_height + ")")
@@ -196,7 +196,7 @@ $ ->
)
#.attr("dy", "-1.0em")
-
+
add_y_axis: () ->
yAxis = d3.svg.axis()
.scale(@y_scale)
@@ -207,7 +207,7 @@ $ ->
.attr("class", "y_axis")
.attr("transform", "translate(" + @x_buffer + ",0)")
.call(yAxis)
-
+
add_chr_lines: () ->
@svg.selectAll("line")
.data(@cumulative_chr_lengths, (d) =>
@@ -241,7 +241,7 @@ $ ->
)
.attr("height", @plot_height-@y_buffer)
.attr("fill", "white")
-
+
add_chr_labels: () ->
chr_names = []
for key of @chromosomes
@@ -265,7 +265,7 @@ $ ->
.attr("font-family", "sans-serif")
.attr("font-size", "18px")
#.attr("fill", "grey")
-
+
connect_markers: () ->
@svg.selectAll("line")
.data(@plot_coordinates)
@@ -290,7 +290,8 @@ $ ->
return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
)
.style("stroke", "black")
-
- console.time('Create manhattan plot')
+
+ console.time('Create interval map')
+ console.log("TESTING")
new Interval_Map(600, 1200)
- console.timeEnd('Create manhattan plot')
\ No newline at end of file
+ console.timeEnd('Create interval map')
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.js b/wqflask/wqflask/static/new/javascript/interval_mapping.js
index 521a1c7a..3a2ce6d7 100644
--- a/wqflask/wqflask/static/new/javascript/interval_mapping.js
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.js
@@ -85,21 +85,21 @@
_ref = js_data.qtl_results;
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
result = _ref[_i];
- if (result.locus.chr === "X") {
+ if (result.chr === "X") {
chr_length = parseFloat(this.chromosomes[20]);
} else {
- chr_length = parseFloat(this.chromosomes[result.locus.chr]);
+ chr_length = parseFloat(this.chromosomes[result.chr]);
}
- if (!(_ref1 = result.locus.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
- chr_seen.push(result.locus.chr);
+ if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
+ chr_seen.push(result.chr);
chr_lengths.push(chr_length);
- if (result.locus.chr !== "1") {
+ if (result.chr !== "1") {
this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
}
}
- this.x_coords.push(this.total_length + parseFloat(result.locus.Mb));
- this.y_coords.push(result.lrs);
- this.marker_names.push(result.locus.name);
+ this.x_coords.push(this.total_length + parseFloat(result.Mb));
+ this.y_coords.push(result.lrs_value);
+ this.marker_names.push(result.name);
}
return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
};
@@ -264,9 +264,10 @@
return Interval_Map;
})();
- console.time('Create manhattan plot');
+ console.time('Create interval map');
+ console.log("TESTING");
new Interval_Map(600, 1200);
- return console.timeEnd('Create manhattan plot');
+ return console.timeEnd('Create interval map');
});
}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 2892987e..f5f13c27 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -49,10 +49,10 @@ $ ->
get_chr_lengths: () ->
###
- Gets a list of both individual and cumulative (the position of one on the graph
- is its own length plus the lengths of all preceding chromosomes) lengths in order
- to draw the vertical lines separating chromosomes and the chromosome labels
-
+ #Gets a list of both individual and cumulative (the position of one on the graph
+ #is its own length plus the lengths of all preceding chromosomes) lengths in order
+ #to draw the vertical lines separating chromosomes and the chromosome labels
+ #
###
console.log("@chromosomes: ", @chromosomes)
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index ffcf1a75..cdf37671 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -57,9 +57,10 @@
Manhattan_Plot.prototype.get_chr_lengths = function() {
/*
- Gets a list of both individual and cumulative (the position of one on the graph
- is its own length plus the lengths of all preceding chromosomes) lengths in order
- to draw the vertical lines separating chromosomes and the chromosome labels
+ #Gets a list of both individual and cumulative (the position of one on the graph
+ #is its own length plus the lengths of all preceding chromosomes) lengths in order
+ #to draw the vertical lines separating chromosomes and the chromosome labels
+ #
*/
var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
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 8571753e..df9bfc9d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -53,6 +53,7 @@ $ ->
return false
$("#interval_mapping_compute").click(() =>
+ console.log("In interval mapping")
$("#progress_bar_container").modal()
url = "/interval_mapping"
form_data = $('#trait_data_form').serialize()
@@ -118,8 +119,12 @@ $ ->
composite_mapping_fields = ->
$(".composite_fields").toggle()
+ mapping_method_fields = ->
+ $(".mapping_method_fields").toggle()
+
$("#use_composite_choice").change(composite_mapping_fields)
+ $("#mapping_method_choice").change(mapping_method_fields)
#### Todo: Redo below so its like submit_special and requires no js hardcoding
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 1153b8ef..b474bd80 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -5,7 +5,7 @@
root = typeof exports !== "undefined" && exports !== null ? exports : this;
$(function() {
- var composite_mapping_fields, get_progress, submit_special, toggle_enable_disable, update_time_remaining,
+ var composite_mapping_fields, get_progress, mapping_method_fields, submit_special, toggle_enable_disable, update_time_remaining,
_this = this;
submit_special = function() {
var url;
@@ -64,6 +64,7 @@
};
$("#interval_mapping_compute").click(function() {
var form_data, url;
+ console.log("In interval mapping");
$("#progress_bar_container").modal();
url = "/interval_mapping";
form_data = $('#trait_data_form').serialize();
@@ -128,7 +129,11 @@
composite_mapping_fields = function() {
return $(".composite_fields").toggle();
};
+ mapping_method_fields = function() {
+ return $(".mapping_method_fields").toggle();
+ };
$("#use_composite_choice").change(composite_mapping_fields);
+ $("#mapping_method_choice").change(mapping_method_fields);
toggle_enable_disable = function(elem) {
return $(elem).prop("disabled", !$(elem).prop("disabled"));
};
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 0360f619..9b98c955 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -212,7 +212,7 @@
-
+
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
index 25de2dc1..e4e08388 100644
--- a/wqflask/wqflask/templates/interval_mapping.html
+++ b/wqflask/wqflask/templates/interval_mapping.html
@@ -1,7 +1,6 @@
{% extends "base.html" %}
{% block title %}Interval Mapping{% endblock %}
{% block css %}
-
@@ -31,7 +30,9 @@
| Index |
LRS Score |
+ {% if method == "qtl_reaper" %}
Additive Effect |
+ {% endif %}
Chr |
Mb |
Locus |
@@ -41,11 +42,13 @@
{% for marker in qtl_results %}
| {{ loop.index }} |
- {{ marker.lrs|float }} |
+ {{ marker.lrs_value|float }} |
+ {% if method == "qtl_reaper" %}
{{ marker.additive|float }} |
- {{ marker.locus.chr|int }} |
- {{ marker.locus.Mb|float }} |
- {{ marker.locus.name }} |
+ {% endif %}
+ {{ marker.chr|int }} |
+ {{ marker.Mb|float }} |
+ {{ marker.name }} |
{% endfor %}
@@ -63,7 +66,7 @@
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 0ad6eedb..86891bb0 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -59,8 +59,8 @@
-
-
+
+
{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index a835a41b..58ee8982 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -16,6 +16,16 @@
+
+
+
+
+
+
+
@@ -28,14 +38,14 @@
-
+
-
+
@@ -44,7 +54,7 @@
-
+