From 6fc0b92ad14bfbc8c752b7730f70c6b22294f667 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 25 Oct 2013 18:16:54 -0500
Subject: Began working on color coding bar chart by extra attributes
---
wqflask/base/data_set.py | 1 +
wqflask/base/trait.py | 6 +++--
wqflask/wqflask/show_trait/SampleList.py | 2 +-
.../static/new/javascript/show_trait.coffee | 23 ++++++++++++++----
.../wqflask/static/new/javascript/show_trait.js | 27 ++++++++++++++++++----
.../templates/show_trait_statistics_new.html | 10 ++++++++
6 files changed, 57 insertions(+), 12 deletions(-)
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index f25e7974..cd8c1ac1 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -224,6 +224,7 @@ class DatasetGroup(object):
"""
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
+ print("dataset name:", dataset.name)
self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
if self.name == 'BXD300':
self.name = "BXD"
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 6a64eeaf..77e451a1 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -382,6 +382,7 @@ class GeneralTrait(object):
#trait_qtl = self.cursor.fetchone()
if trait_qtl:
self.locus, self.lrs, self.pvalue, self.mean = trait_qtl
+ print("self.locus:", self.locus)
if self.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
@@ -390,8 +391,9 @@ class GeneralTrait(object):
Geno.SpeciesId = Species.Id
""".format(self.dataset.group.species, self.locus)
result = g.db.execute(query).fetchone()
- self.locus_chr = result[0]
- self.locus_mb = result[1]
+ if result:
+ self.locus_chr = result[0]
+ self.locus_mb = result[1]
else:
self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = ""
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 1130fb60..9cd7d895 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -138,7 +138,7 @@ class SampleList(object):
StrainId = %s AND
CaseAttributeId = %s
group by CaseAttributeXRef.CaseAttributeId""", (
- self.this_trait.db.id, sample_id, str(attribute)))
+ self.this_trait.dataset.id, sample_id, str(attribute)))
attribute_value = result.fetchone().Value #Trait-specific attributes, if any
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 2e049e6a..bf01ee5d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -83,6 +83,10 @@ $ ->
@create_scales()
@create_graph()
+ d3.select("#color_attribute").on("change", =>
+
+ )
+
d3.select("#update_bar_chart").on("click", =>
if $("#update_bar_chart").html() == 'Sort By Value'
$("#update_bar_chart").html('Sort By Name')
@@ -99,10 +103,14 @@ $ ->
.attr("height", (d) =>
return @plot_height - @y_scale(d[1])
)
+ .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)
- .rangeRoundBands([0, @plot_width], .1)
+ .rangeBands([0, @plot_width], .1)
$('.x.axis').remove()
@add_x_axis(x_scale)
else
@@ -117,17 +125,24 @@ $ ->
.attr("height", (d) =>
return @plot_height - @y_scale(d)
)
+ .select("title")
+ .text((d) =>
+ return d
+ )
x_scale = d3.scale.ordinal()
.domain(@sample_names)
- .rangeRoundBands([0, @plot_width], .1)
+ .rangeBands([0, @plot_width], .1)
$('.x.axis').remove()
@add_x_axis(x_scale)
-
)
get_samples: () ->
@sample_names = (sample.name for sample in @sample_list when sample.value != null)
@sample_vals = (sample.value for sample in @sample_list when sample.value != null)
+ attributes = (key for key of @sample_list[0]["extra_attributes"])
+ console.log("attributes:", attributes)
+ if attributes.length > 0
+ alert("TEST")
create_svg: () ->
svg = d3.select("#bar_chart")
@@ -143,7 +158,7 @@ $ ->
create_scales: () ->
@x_scale = d3.scale.ordinal()
.domain(@sample_names)
- .rangeRoundBands([0, @plot_width], .1)
+ .rangeBands([0, @plot_width], .1)
@y_scale = d3.scale.linear()
.domain([@y_min * 0.75, @y_max])
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index e6fcbd7b..7b5e4b88 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -92,6 +92,7 @@
this.plot_height -= this.y_buffer;
this.create_scales();
this.create_graph();
+ d3.select("#color_attribute").on("change", function() {});
d3.select("#update_bar_chart").on("click", function() {
var sortItems, sorted_sample_names, x_scale;
if ($("#update_bar_chart").html() === 'Sort By Value') {
@@ -103,6 +104,8 @@
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];
});
sorted_sample_names = (function() {
var _i, _len, _ref, _results;
@@ -114,7 +117,7 @@
}
return _results;
}).call(_this);
- x_scale = d3.scale.ordinal().domain(sorted_sample_names).rangeRoundBands([0, _this.plot_width], .1);
+ 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);
} else {
@@ -123,8 +126,10 @@
return _this.y_scale(d);
}).attr("height", function(d) {
return _this.plot_height - _this.y_scale(d);
+ }).select("title").text(function(d) {
+ return d;
});
- x_scale = d3.scale.ordinal().domain(_this.sample_names).rangeRoundBands([0, _this.plot_width], .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);
}
@@ -132,7 +137,7 @@
}
Histogram.prototype.get_samples = function() {
- var sample;
+ var attributes, key, sample;
this.sample_names = (function() {
var _i, _len, _ref, _results;
_ref = this.sample_list;
@@ -145,7 +150,7 @@
}
return _results;
}).call(this);
- return this.sample_vals = (function() {
+ this.sample_vals = (function() {
var _i, _len, _ref, _results;
_ref = this.sample_list;
_results = [];
@@ -157,6 +162,18 @@
}
return _results;
}).call(this);
+ attributes = (function() {
+ var _results;
+ _results = [];
+ for (key in this.sample_list[0]["extra_attributes"]) {
+ _results.push(key);
+ }
+ return _results;
+ }).call(this);
+ console.log("attributes:", attributes);
+ if (attributes.length > 0) {
+ return alert("TEST");
+ }
};
Histogram.prototype.create_svg = function() {
@@ -166,7 +183,7 @@
};
Histogram.prototype.create_scales = function() {
- this.x_scale = d3.scale.ordinal().domain(this.sample_names).rangeRoundBands([0, this.plot_width], .1);
+ this.x_scale = d3.scale.ordinal().domain(this.sample_names).rangeBands([0, this.plot_width], .1);
return this.y_scale = d3.scale.linear().domain([this.y_min * 0.75, this.y_max]).range([this.plot_height, this.y_buffer]);
};
diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html
index acd6cc62..58389ce4 100644
--- a/wqflask/wqflask/templates/show_trait_statistics_new.html
+++ b/wqflask/wqflask/templates/show_trait_statistics_new.html
@@ -7,6 +7,16 @@
{% endfor %}
+ {% if sample_groups[0].attributes %}
+
+
+
+ {% endif %}