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-rwxr-xr-xwqflask/base/trait.py28
-rwxr-xr-xwqflask/wqflask/static/new/javascript/histogram.coffee27
-rwxr-xr-xwqflask/wqflask/static/new/javascript/histogram.js245
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait.coffee1
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait.js1
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html10
-rwxr-xr-xwqflask/wqflask/templates/show_trait_details.html6
7 files changed, 181 insertions, 137 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index f3648b80..8930c917 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -53,7 +53,8 @@ class GeneralTrait(object):
self.pvalue = None
self.mean = None
self.num_overlap = None
-
+ self.strand_probe = None
+ self.symbol = None
if kw.get('fullname'):
name2 = value.split("::")
@@ -533,12 +534,27 @@ class GeneralTrait(object):
return setDescription
@property
+ def name_header_fmt(self):
+ '''Return a human-readable name for use in page header'''
+ if self.dataset.type == 'ProbeSet':
+ return self.symbol
+ elif self.dataset.type == 'Geno':
+ return self.name
+ elif self.dataset.type == 'Publish':
+ return self.post_publication_abbreviation
+ else:
+ return "unnamed"
+
+ @property
def description_fmt(self):
'''Return a text formated description'''
- if self.description:
- formatted = self.description
- if self.probe_target_description:
- formatted += "; " + self.probe_target_description
+ if self.dataset.type == 'ProbeSet':
+ if self.description:
+ formatted = self.description
+ if self.probe_target_description:
+ formatted += "; " + self.probe_target_description
+ elif self.dataset.type == 'Publish':
+ formatted = self.post_publication_description
else:
formatted = "Not available"
return formatted.capitalize()
@@ -652,4 +668,4 @@ def get_sample_data():
# jsonable_sample_data[sample] = trait_ob.data[sample].value
#
#return jsonable_sample_data
- \ No newline at end of file
+
diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index 98f89ac6..68d9b5a2 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -4,7 +4,6 @@ class Histogram
constructor: (@sample_list, @sample_group) ->
@sort_by = "name"
@format_count = d3.format(",.0f") #a formatter for counts
- @get_sample_vals()
@margin = {top: 10, right: 30, bottom: 30, left: 30}
@plot_width = 960 - @margin.left - @margin.right
@@ -12,21 +11,25 @@ class Histogram
@x_buffer = @plot_width/20
@y_buffer = @plot_height/20
+ @plot_height -= @y_buffer
+
+ @get_sample_vals(@sample_list)
+ @redraw(@sample_vals)
+ redraw: (@sample_vals) ->
@y_min = d3.min(@sample_vals)
@y_max = d3.max(@sample_vals) * 1.1
-
- @plot_height -= @y_buffer
+
@create_x_scale()
@get_histogram_data()
@create_y_scale()
+ $("#histogram").empty()
@svg = @create_svg()
-
@create_graph()
- get_sample_vals: () ->
- @sample_vals = (sample.value for sample in @sample_list when sample.value != null)
+ get_sample_vals: (sample_list) ->
+ @sample_vals = (sample.value for sample in sample_list when sample.value != null)
create_svg: () ->
svg = d3.select("#histogram")
@@ -53,8 +56,9 @@ class Histogram
get_histogram_data: () ->
console.log("sample_vals:", @sample_vals)
+ n_bins = Math.sqrt(@sample_vals.length)
@histogram_data = d3.layout.histogram()
- .bins(@x_scale.ticks(20))(@sample_vals)
+ .bins(@x_scale.ticks(n_bins))(@sample_vals)
console.log("histogram_data:", @histogram_data[0])
create_y_scale: () ->
@@ -112,17 +116,20 @@ class Histogram
.attr("class", "bar")
.attr("transform", (d) =>
return "translate(" + @x_scale(d.x) + "," + @y_scale(d.y) + ")")
+
+ rect_width = @x_scale(@histogram_data[0].x + @histogram_data[0].dx) -
+ @x_scale(@histogram_data[0].x)
bar.append("rect")
.attr("x", 1)
- .attr("width", @x_scale(@histogram_data[0].x + @histogram_data[0].dx) - 1)
+ .attr("width", rect_width - 1)
.attr("height", (d) =>
return @plot_height - @y_scale(d.y)
)
bar.append("text")
.attr("dy", ".75em")
.attr("y", 6)
- .attr("x", @x_scale(@histogram_data[0].dx)/2)
+ .attr("x", rect_width / 2)
.attr("text-anchor", "middle")
.style("fill", "#fff")
.text((d) =>
@@ -131,4 +138,4 @@ class Histogram
return @format_count(d.y)
)
-root.Histogram = Histogram \ No newline at end of file
+root.Histogram = Histogram
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index 561a3068..d872a3ba 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -1,124 +1,135 @@
-// Generated by CoffeeScript 1.8.0
-var Histogram, root;
-
-root = typeof exports !== "undefined" && exports !== null ? exports : this;
-
-Histogram = (function() {
- function Histogram(sample_list, sample_group) {
- this.sample_list = sample_list;
- this.sample_group = sample_group;
- this.sort_by = "name";
- this.format_count = d3.format(",.0f");
- this.get_sample_vals();
- this.margin = {
- top: 10,
- right: 30,
- bottom: 30,
- left: 30
+// Generated by CoffeeScript 1.9.2
+(function() {
+ var Histogram, root;
+
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+ Histogram = (function() {
+ function Histogram(sample_list1, sample_group) {
+ this.sample_list = sample_list1;
+ this.sample_group = sample_group;
+ this.sort_by = "name";
+ this.format_count = d3.format(",.0f");
+ this.margin = {
+ top: 10,
+ right: 30,
+ bottom: 30,
+ left: 30
+ };
+ this.plot_width = 960 - this.margin.left - this.margin.right;
+ this.plot_height = 500 - this.margin.top - this.margin.bottom;
+ this.x_buffer = this.plot_width / 20;
+ this.y_buffer = this.plot_height / 20;
+ this.plot_height -= this.y_buffer;
+ this.get_sample_vals(this.sample_list);
+ this.redraw(this.sample_vals);
+ }
+
+ Histogram.prototype.redraw = function(sample_vals) {
+ this.sample_vals = sample_vals;
+ this.y_min = d3.min(this.sample_vals);
+ this.y_max = d3.max(this.sample_vals) * 1.1;
+ this.create_x_scale();
+ this.get_histogram_data();
+ this.create_y_scale();
+ $("#histogram").empty();
+ this.svg = this.create_svg();
+ return this.create_graph();
};
- this.plot_width = 960 - this.margin.left - this.margin.right;
- this.plot_height = 500 - this.margin.top - this.margin.bottom;
- this.x_buffer = this.plot_width / 20;
- this.y_buffer = this.plot_height / 20;
- this.y_min = d3.min(this.sample_vals);
- this.y_max = d3.max(this.sample_vals) * 1.1;
- this.plot_height -= this.y_buffer;
- this.create_x_scale();
- this.get_histogram_data();
- this.create_y_scale();
- this.svg = this.create_svg();
- this.create_graph();
- }
-
- Histogram.prototype.get_sample_vals = function() {
- var sample;
- return this.sample_vals = (function() {
- var _i, _len, _ref, _results;
- _ref = this.sample_list;
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- if (sample.value !== null) {
- _results.push(sample.value);
+
+ Histogram.prototype.get_sample_vals = function(sample_list) {
+ var sample;
+ return this.sample_vals = (function() {
+ var i, len, results;
+ results = [];
+ for (i = 0, len = sample_list.length; i < len; i++) {
+ sample = sample_list[i];
+ if (sample.value !== null) {
+ results.push(sample.value);
+ }
}
- }
- return _results;
- }).call(this);
- };
-
- Histogram.prototype.create_svg = function() {
- var svg;
- svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
- return svg;
- };
-
- Histogram.prototype.create_x_scale = function() {
- var x0;
- console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
- x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
- return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
- };
-
- Histogram.prototype.get_histogram_data = function() {
- console.log("sample_vals:", this.sample_vals);
- this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(20))(this.sample_vals);
- return console.log("histogram_data:", this.histogram_data[0]);
- };
-
- Histogram.prototype.create_y_scale = function() {
- return this.y_scale = d3.scale.linear().domain([
- 0, d3.max(this.histogram_data, (function(_this) {
+ return results;
+ })();
+ };
+
+ Histogram.prototype.create_svg = function() {
+ var svg;
+ svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
+ return svg;
+ };
+
+ Histogram.prototype.create_x_scale = function() {
+ var x0;
+ console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
+ x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
+ return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
+ };
+
+ Histogram.prototype.get_histogram_data = function() {
+ var n_bins;
+ console.log("sample_vals:", this.sample_vals);
+ n_bins = Math.sqrt(this.sample_vals.length);
+ this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(n_bins))(this.sample_vals);
+ return console.log("histogram_data:", this.histogram_data[0]);
+ };
+
+ Histogram.prototype.create_y_scale = function() {
+ return this.y_scale = d3.scale.linear().domain([
+ 0, d3.max(this.histogram_data, (function(_this) {
+ return function(d) {
+ return d.y;
+ };
+ })(this))
+ ]).range([this.plot_height, 0]);
+ };
+
+ Histogram.prototype.create_graph = function() {
+ this.add_x_axis();
+ this.add_y_axis();
+ return this.add_bars();
+ };
+
+ Histogram.prototype.add_x_axis = function() {
+ var x_axis;
+ x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom");
+ return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
+ };
+
+ Histogram.prototype.add_y_axis = function() {
+ var yAxis;
+ yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+ return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
+ };
+
+ Histogram.prototype.add_bars = function() {
+ var bar, rect_width;
+ console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
+ bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) {
return function(d) {
- return d.y;
+ return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
};
- })(this))
- ]).range([this.plot_height, 0]);
- };
-
- Histogram.prototype.create_graph = function() {
- this.add_x_axis();
- this.add_y_axis();
- return this.add_bars();
- };
-
- Histogram.prototype.add_x_axis = function() {
- var x_axis;
- x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom");
- return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
- };
-
- Histogram.prototype.add_y_axis = function() {
- var yAxis;
- yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
- return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
- };
-
- Histogram.prototype.add_bars = function() {
- var bar;
- console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
- bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) {
- return function(d) {
- return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
- };
- })(this));
- bar.append("rect").attr("x", 1).attr("width", this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - 1).attr("height", (function(_this) {
- return function(d) {
- return _this.plot_height - _this.y_scale(d.y);
- };
- })(this));
- return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", this.x_scale(this.histogram_data[0].dx) / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
- return function(d) {
- var bar_height;
- bar_height = _this.plot_height - _this.y_scale(d.y);
- if (bar_height > 20) {
- return _this.format_count(d.y);
- }
- };
- })(this));
- };
+ })(this));
+ rect_width = this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - this.x_scale(this.histogram_data[0].x);
+ bar.append("rect").attr("x", 1).attr("width", rect_width - 1).attr("height", (function(_this) {
+ return function(d) {
+ return _this.plot_height - _this.y_scale(d.y);
+ };
+ })(this));
+ return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", rect_width / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
+ return function(d) {
+ var bar_height;
+ bar_height = _this.plot_height - _this.y_scale(d.y);
+ if (bar_height > 20) {
+ return _this.format_count(d.y);
+ }
+ };
+ })(this));
+ };
+
+ return Histogram;
- return Histogram;
+ })();
-})();
+ root.Histogram = Histogram;
-root.Histogram = Histogram;
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index ee57831f..1d3123ba 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -238,6 +238,7 @@ $ ->
sample_sets['samples_all'].add_value(real_value)
already_seen[name] = true
console.log("towards end:", sample_sets)
+ root.histogram.redraw(sample_sets['samples_primary'].the_values)
update_stat_values(sample_sets)
show_hide_outliers = ->
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index c2dc07ee..9323862a 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -265,6 +265,7 @@
}
}
console.log("towards end:", sample_sets);
+ root.histogram.redraw(sample_sets['samples_primary'].the_values);
return update_stat_values(sample_sets);
};
show_hide_outliers = function() {
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index a1723ef8..d6f22f41 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -13,8 +13,12 @@
{% endblock %}
{% block content %} <!-- Start of body -->
- {{ header("{}".format(this_trait.symbol),
- '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+ {% if this_trait.dataset.type != 'Geno' %}
+ {{ header("{}".format(this_trait.name_header_fmt),
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+ {% else %}
+ {{ header("{}".format(this_trait.name_header_fmt)) }}
+ {% endif %}
<form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
@@ -31,7 +35,7 @@
<div class="page-header">
<h1>{{ dataset.group.species.capitalize() }} -
{{ dataset.group.name }} -
- {{ this_trait.symbol }}
+ {{ this_trait.name_header_fmt }}
</h1>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 0afac1f7..e1780e42 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,9 +1,13 @@
<dl class="dl-horizontal">
+ {% if this_trait.dataset.type == 'ProbeSet' %}
<dt>Aliases</dt>
<dd>{{ this_trait.alias_fmt }}</dd>
+ {% endif %}
+ {% if this_trait.dataset.type != 'Publish' %}
<dt>Location</dt>
<dd>{{ this_trait.location_fmt }}</dd>
+ {% endif %}
<dt>Database</dt>
<dd>
@@ -16,7 +20,7 @@
<dt>
<a href="/blatInfo.html" target="_blank"
title="Values higher than 2 for the specificity are good">
- BLAT Specifity
+ BLAT Specificity
</a>
</dt>
<dd>{{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}</dd>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 09:43:57 +0000