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-rwxr-xr-xwqflask/base/data_set.py14
-rwxr-xr-xwqflask/base/trait.py63
-rw-r--r--wqflask/wqflask/collect.py30
-rw-r--r--wqflask/wqflask/interval_mapping/__init__.py0
-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py180
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py1
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py2
-rw-r--r--wqflask/wqflask/static/new/css/interval_mapping.css32
-rw-r--r--wqflask/wqflask/static/new/css/marker_regression.css4
-rw-r--r--wqflask/wqflask/static/new/javascript/bar_chart.coffee356
-rw-r--r--wqflask/wqflask/static/new/javascript/bar_chart.js210
-rw-r--r--wqflask/wqflask/static/new/javascript/box_plot.coffee45
-rw-r--r--wqflask/wqflask/static/new/javascript/box_plot.js83
-rw-r--r--wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee73
-rw-r--r--wqflask/wqflask/static/new/javascript/get_traits_from_collection.js82
-rw-r--r--wqflask/wqflask/static/new/javascript/interval_mapping.coffee297
-rw-r--r--wqflask/wqflask/static/new/javascript/interval_mapping.js273
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.coffee8
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.js7
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.coffee442
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js484
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee31
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js34
-rw-r--r--wqflask/wqflask/static/new/packages/DataTables/js/dataTables.scientific.js13
-rw-r--r--wqflask/wqflask/templates/base.html2
-rw-r--r--wqflask/wqflask/templates/collections/list.html11
-rw-r--r--wqflask/wqflask/templates/interval_mapping.html107
-rw-r--r--wqflask/wqflask/templates/show_trait.html6
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html26
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics_new.html21
-rw-r--r--wqflask/wqflask/user_manager.py30
-rw-r--r--wqflask/wqflask/views.py30
32 files changed, 1852 insertions, 1145 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cd8c1ac1..fbe78d5d 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -318,12 +318,17 @@ class DatasetGroup(object):
#determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
- self.genotype = genotype_2
+ #self.genotype = genotype_2
+ genotype = genotype_2
else:
self.incparentsf1 = 0
- self.genotype = genotype_1
+ #self.genotype = genotype_1
+ genotype = genotype_1
- self.samplelist = list(self.genotype.prgy)
+ #self.samplelist = list(self.genotype.prgy)
+ self.samplelist = list(genotype.prgy)
+
+ return genotype
#class DataSets(object):
@@ -624,7 +629,7 @@ class PhenotypeDataSet(DataSet):
description = this_trait.pre_publication_description
- this_trait.description_display = description
+ this_trait.description_display = description.strip()
if not this_trait.year.isdigit():
this_trait.pubmed_text = "N/A"
@@ -1084,6 +1089,7 @@ class MrnaAssayDataSet(DataSet):
Strain.Name
""" % (escape(trait), escape(self.name))
results = g.db.execute(query).fetchall()
+ print("RETRIEVED RESULTS HERE:", results)
return results
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 731f99eb..712d9af5 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -12,10 +12,13 @@ from base.data_set import create_dataset
from dbFunction import webqtlDatabaseFunction
from utility import webqtlUtil
+from wqflask import app
+
+import simplejson as json
from MySQLdb import escape_string as escape
from pprint import pformat as pf
-from flask import Flask, g
+from flask import Flask, g, request
def print_mem(stage=""):
mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
@@ -43,7 +46,7 @@ class GeneralTrait(object):
self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet
self.data = kw.get('data', {})
- # Sets defaultst
+ # Sets defaults
self.locus = None
self.lrs = None
self.pvalue = None
@@ -63,6 +66,17 @@ class GeneralTrait(object):
# So we could add a simple if statement to short-circuit this if necessary
self.retrieve_info(get_qtl_info=get_qtl_info)
self.retrieve_sample_data()
+
+
+ def jsonable(self):
+ """Return a dict suitable for using as json
+
+ Actual turning into json doesn't happen here though"""
+ return dict(name=self.name,
+ dataset=self.dataset.name,
+ description=self.description_display,
+ mean=self.mean)
+
def get_info(self):
"""For lots of traits just use get_trait_info in dataset instead...that will be way
@@ -154,7 +168,7 @@ class GeneralTrait(object):
result.append(None)
return result
- def export_informative(self, incVar=0):
+ def export_informative(self, include_variance=0):
"""
export informative sample
mostly used in qtl regression
@@ -163,12 +177,12 @@ class GeneralTrait(object):
samples = []
vals = []
the_vars = []
- for sample, value in self.data.items():
- if value.val != None:
- if not incVar or value.var != None:
- samples.append(sample)
- vals.append(value.val)
- the_vars.append(value.var)
+ for sample_name, sample_data in self.data.items():
+ if sample_data.value != None:
+ if not include_variance or sample_data.variance != None:
+ samples.append(sample_name)
+ vals.append(sample_data.value)
+ the_vars.append(sample_data.variance)
return samples, vals, the_vars
@@ -235,11 +249,19 @@ class GeneralTrait(object):
# Todo: is this necessary? If not remove
self.data.clear()
+ if self.dataset.group.parlist:
+ all_samples_ordered = (self.dataset.group.parlist +
+ self.dataset.group.f1list +
+ self.dataset.group.samplelist)
+ elif self.dataset.group.f1list:
+ all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
+ else:
+ all_samples_ordered = self.dataset.group.samplelist
+
if results:
for item in results:
- #name, value, variance, num_cases = item
+ name, value, variance, num_cases = item
if not samplelist or (samplelist and name in samplelist):
- name = item[0]
self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
#def keys(self):
@@ -608,3 +630,22 @@ class GeneralTrait(object):
ZValue = 0.5*log((1.0+self.correlation)/(1.0-self.correlation))
ZValue = ZValue*sqrt(self.overlap-3)
self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))
+
+
+
+@app.route("/trait/get_sample_data")
+def get_sample_data():
+ params = request.args
+ trait = params['trait']
+ dataset = params['dataset']
+
+ trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
+
+ return json.dumps({key: value.value for key, value in trait_ob.data.iteritems() })
+
+ #jsonable_sample_data = {}
+ #for sample in trait_ob.data.iteritems():
+ # jsonable_sample_data[sample] = trait_ob.data[sample].value
+ #
+ #return jsonable_sample_data
+ \ No newline at end of file
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index ef7b37df..48b4b4da 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -23,7 +23,7 @@ Redis = redis.StrictRedis()
from flask import (Flask, g, render_template, url_for, request, make_response,
- redirect, flash)
+ redirect, flash, jsonify)
from wqflask import app
@@ -122,16 +122,18 @@ def create_new():
@app.route("/collections/list")
def list_collections():
+ params = request.args
user_collections = g.user_session.user_ob.user_collections
return render_template("collections/list.html",
+ params = params,
user_collections = user_collections,
)
-
@app.route("/collections/view")
def view_collection():
params = request.args
+ print("params in view collection:", params)
uc_id = params['uc_id']
uc = model.UserCollection.query.get(uc_id)
traits = json.loads(uc.members)
@@ -139,6 +141,7 @@ def view_collection():
print("in view_collection traits are:", traits)
trait_obs = []
+ json_version = []
for atrait in traits:
name, dataset_name = atrait.split(':')
@@ -146,8 +149,23 @@ def view_collection():
trait_ob = trait.GeneralTrait(name=name, dataset_name=dataset_name)
trait_ob.get_info()
trait_obs.append(trait_ob)
-
- return render_template("collections/view.html",
- trait_obs=trait_obs,
- uc = uc,
+
+ json_version.append(trait_ob.jsonable())
+ #json_version.append(dict(name=trait_ob.name,
+ # description=trait_ob.description_display,
+ # location=trait_ob.location_repr,
+ # mean=trait_ob.mean,
+ # lrs_score=trait_ob.LRS_score_repr,
+ # lrs_location=trait_ob.LRS_location_repr))
+ # dis=trait_ob.description))
+ #json_version.append(trait_ob.__dict__th)
+
+ collection_info = dict(trait_obs=trait_obs,
+ uc = uc)
+ if "json" in params:
+ print("json_version:", json_version)
+ return json.dumps(json_version)
+ else:
+ return render_template("collections/view.html",
+ **collection_info
)
diff --git a/wqflask/wqflask/interval_mapping/__init__.py b/wqflask/wqflask/interval_mapping/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/wqflask/interval_mapping/__init__.py
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index aca99cbe..f0985cc2 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -51,85 +51,169 @@ class IntervalMapping(object):
self.samples.append(str(sample))
self.vals.append(value)
+ print("start_vars:", start_vars)
+
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 = {}
for key in self.species.chromosomes.chromosomes.keys():
chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
+ #print("self.qtl_results:", self.qtl_results)
+
self.js_data = dict(
- lrs_lod = self.lrs_lod,
chromosomes = chromosome_mb_lengths,
qtl_results = self.qtl_results,
+ #lrs_lod = self.lrs_lod,
)
def set_options(self, start_vars):
"""Sets various options (physical/genetic mapping, # permutations, which chromosome"""
- self.plot_scale = start_vars['scale']
+ #self.plot_scale = start_vars['scale']
#if self.plotScale == 'physic' and not fd.genotype.Mbmap:
# self.plotScale = 'morgan'
- self.num_permutations = start_vars['num_permutations']
- self.do_bootstrap = start_vars['do_bootstrap']
- self.control_locus = start_vars['control_locus']
- self.selected_chr = start_vars['selected_chr']
- self.weighted_regression = start_vars['weighted']
- self.lrs_lod = start_vars['lrs_lod']
+ 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']
+ if 'control_locus' in start_vars:
+ self.control_locus = start_vars['control_locus']
+ else:
+ self.control_locus = None
+ #self.weighted_regression = start_vars['weighted']
+ #self.lrs_lod = start_vars['lrs_lod']
def gen_qtl_results(self, tempdata):
"""Generates qtl results for plotting interval map"""
self.dataset.group.get_markers()
- self.dataset.read_genotype_file()
+ 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])
+
+ #if self.weighted_regression:
+ # self.lrs_array = self.genotype.permutation(strains = trimmed_samples,
+ # trait = trimmed_values,
+ # variance = _vars,
+ # nperm=self.num_permutations)
+ #else:
+ 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)
- samples, values, variances = self.trait.export_informative()
if self.control_locus:
- if self.weighted_regression:
- self.qtl_results = self.dataset.genotype.regression(strains = samples,
- trait = values,
- variance = variances,
- control = self.control_locus)
- else:
- self.qtl_results = self.dataset.genotype.regression(strains = samples,
- trait = values,
- control = self.control_locus)
+ #if self.weighted_regression:
+ # self.qtl_results = self.dataset.genotype.regression(strains = samples,
+ # trait = values,
+ # variance = variances,
+ # control = self.control_locus)
+ #else:
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values,
+ control = self.control_locus)
else:
- if self.weighted_regression:
- self.qtl_results = self.dataset.genotype.regression(strains = samples,
- trait = values,
- variance = variances)
- else:
- self.qtl_results = self.dataset.genotype.regression(strains = samples,
- trait = values)
+ #if self.weighted_regression:
+ # self.qtl_results = self.dataset.genotype.regression(strains = samples,
+ # trait = values,
+ # variance = variances)
+ #else:
+ print("strains:", trimmed_samples)
+ print("trait:", trimmed_values)
+ 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": 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/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 6ef1669b..60d36b8d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -107,8 +107,6 @@ def run_human(pheno_vector,
with Bench("Create list of inputs"):
inputs = list(plink_input)
-
- print("len(genotypes): ", len(inputs))
with Bench("Divide into chunks"):
results = chunks.divide_into_chunks(inputs, 64)
diff --git a/wqflask/wqflask/static/new/css/interval_mapping.css b/wqflask/wqflask/static/new/css/interval_mapping.css
new file mode 100644
index 00000000..5ebf7742
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/interval_mapping.css
@@ -0,0 +1,32 @@
+.interval_map .y_axis path,
+.interval_map .y_axis line {
+ fill: none;
+ stroke: black;
+ shape-rendering: crispEdges;
+}
+.interval_map .y_axis text {
+ font-family: sans-serif;
+ font-size: 14px;
+}
+
+.interval_map .x_axis path,
+.interval_map .x_axis line {
+ fill: none;
+ stroke: black;
+ shape-rendering: crispEdges;
+}
+.interval_map .x_axis text {
+ text-anchor: end;
+ font-family: sans-serif;
+ font-size: 8px;
+}
+
+interval_map rect {
+ stroke: WhiteSmoke;
+ fill: white;
+}
+
+interval_map path {
+ stroke: steelblue;
+ stroke-width: 1;
+} \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index 054ef93e..a737c97e 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -21,10 +21,10 @@
font-size: 8px;
}
-rect {
+/*rect {
stroke: WhiteSmoke;
fill: lightgrey;
-}
+}*/
/*rect {
stroke: WhiteSmoke;
fill: Azure;
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
index 749a7dc0..e1bb36e1 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
@@ -2,11 +2,12 @@ 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
@get_distinct_attr_vals()
- @get_attr_color_dict()
+ @get_attr_color_dict(@distinct_attr_vals)
#Used to calculate the bottom margin so sample names aren't cut off
longest_sample_name = d3.max(sample.length for sample in @sample_names)
@@ -28,17 +29,19 @@ class Bar_Chart
@create_graph()
d3.select("#color_attribute").on("change", =>
- attribute = $("#color_attribute").val()
- if $("#update_bar_chart").html() == 'Sort By Name'
+ @attribute = $("#color_attribute").val()
+ console.log("attr_color_dict:", @attr_color_dict)
+ #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) =>
@@ -50,82 +53,196 @@ 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])
)
-
-
- d3.select("#update_bar_chart").on("click", =>
- if @attributes.length > 0
- attribute = $("#color_attribute").val()
- if $("#update_bar_chart").html() == 'Sort By Value'
- $("#update_bar_chart").html('Sort By Name')
- 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)
- else
- $("#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_value").on("click", =>
+ console.log("sorting by value")
+ @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")
+ @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()
+ # console.log("sort_by: ", sort_by)
+ # if @attributes.length > 0
+ # attribute = $("#color_attribute").val()
+ # if sort_by = "value"
+ # 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)
+ # $('.x.axis').remove()
+ # @add_x_axis(x_scale)
+ # else
+ # console.log("sorting by name")
+ # #$("#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)
+ #)
+
+ d3.select("#color_by_trait").on("click", =>
+ @open_trait_selection()
+
+ )
+
+
+ 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: () ->
+ get_attr_color_dict: (vals) ->
@attr_color_dict = {}
- console.log("distinct_attr_vals:", @distinct_attr_vals)
- for own key, distinct_vals of @distinct_attr_vals
+ console.log("vals:", vals)
+ for own key, distinct_vals of vals
this_color_dict = {}
if distinct_vals.length < 10
color = d3.scale.category10()
@@ -133,6 +250,8 @@ class Bar_Chart
this_color_dict[value] = color(i)
else
console.log("distinct_values:", distinct_vals)
+ #Check whether all values are numbers, and if they are get a corresponding
+ #color gradient
if _.every(distinct_vals, (d) =>
if isNaN(d)
return false
@@ -142,13 +261,24 @@ class Bar_Chart
color_range = d3.scale.linear()
.domain([d3.min(distinct_vals),
d3.max(distinct_vals)])
- .range([0,4])
+ .range([0,255])
for value, i in distinct_vals
- console.log("color_range(value):", color_range(parseInt(value)))
- this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)))
+ console.log("color_range(value):", parseInt(color_range(value)))
+ this_color_dict[value] = d3.rgb(parseInt(color_range(value)),0, 0)
+ #this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)))
#this_color_dict[value] = "rgb(0, 0, " + color_range(parseInt(value)) + ")"
@attr_color_dict[key] = this_color_dict
+ convert_into_colors: (values) ->
+ color_range = d3.scale.linear()
+ .domain([d3.min(values),
+ d3.max(values)])
+ .range([0,255])
+ for value, i in values
+ console.log("color_range(value):", color_range(parseInt(value)))
+ this_color_dict[value] = d3.rgb(color_range(parseInt(value)),0, 0)
+ #this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)))
+
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)
@@ -272,7 +402,7 @@ class Bar_Chart
.attr("height", 100)
.attr("width", 100)
.attr('transform', 'translate(-20,50)')
-
+
legend_rect = legend.selectAll('rect')
.data(distinct_vals)
.enter()
@@ -287,7 +417,7 @@ class Bar_Chart
console.log("TEST:", @attr_color_dict[attribute][d])
return @attr_color_dict[attribute][d]
)
-
+
legend_text = legend.selectAll('text')
.data(distinct_vals)
.enter()
@@ -300,19 +430,63 @@ class Bar_Chart
return d
)
-
- color_by_trait: () ->
- console.log("Before load")
- $('#collections_holder').load('/collections/list #collections_list')
- $.colorbox(
- inline: true
- href: "#collections_holder"
+ open_trait_selection: () ->
+ $('#collections_holder').load('/collections/list?color_by_trait #collections_list', =>
+ $.colorbox(
+ inline: true
+ href: "#collections_holder"
+ )
+ #Removes the links from the collection names, because clicking them would leave the page
+ #instead of loading the list of traits in the colorbox
+ $('a.collection_name').attr( 'onClick', 'return false' )
+ #$('.collection_name').each (index, element) =>
+ # console.log("contents:", $(element).contents())
+ # $(element).contents().unwrap()
)
- console.log("After load")
- #$.colorbox({href:"/collections/list"})
- #$.get(
- # url: /collections/list
- #
- #)
+ color_by_trait: (trait_sample_data) ->
+ console.log("BXD1:", trait_sample_data["BXD1"])
+ console.log("trait_sample_data:", trait_sample_data)
+ trimmed_samples = @trim_values(trait_sample_data)
+ distinct_values = {}
+ distinct_values["collection_trait"] = @get_distinct_values(trimmed_samples)
+ @get_attr_color_dict(distinct_values)
+ if $("#update_bar_chart").html() == 'Sort By Name'
+ @svg.selectAll(".bar")
+ .data(@sorted_samples())
+ .transition()
+ .duration(1000)
+ .style("fill", (d) =>
+ return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]]
+ )
+ .select("title")
+ .text((d) =>
+ return d[1]
+ )
+ else
+ @svg.selectAll(".bar")
+ .data(@samples)
+ .transition()
+ .duration(1000)
+ .style("fill", (d) =>
+ return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]]
+ )
+
+
+ trim_values: (trait_sample_data) ->
+ trimmed_samples = {}
+ for sample in @sample_names
+ if sample of trait_sample_data
+ trimmed_samples[sample] = trait_sample_data[sample]
+ console.log("trimmed_samples:", trimmed_samples)
+ return trimmed_samples
+
+ get_distinct_values: (samples) ->
+ distinct_values = _.uniq(_.values(samples))
+ console.log("distinct_values:", distinct_values)
+ return distinct_values
+ #distinct_values = []
+ #for sample in samples
+ # if samples[sample] in distinct_values
+
root.Bar_Chart = Bar_Chart \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js
index 20fab15c..b02ee1da 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.js
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.js
@@ -13,11 +13,12 @@
_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) {
this.get_distinct_attr_vals();
- this.get_attr_color_dict();
+ this.get_attr_color_dict(this.distinct_attr_vals);
}
longest_sample_name = d3.max((function() {
var _i, _len, _ref, _results;
@@ -46,97 +47,94 @@
this.create_scales();
this.create_graph();
d3.select("#color_attribute").on("change", function() {
- var attribute;
- attribute = $("#color_attribute").val();
- if ($("#update_bar_chart").html() === 'Sort By Name') {
+ _this.attribute = $("#color_attribute").val();
+ console.log("attr_color_dict:", _this.attr_color_dict);
+ 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]);
});
- d3.select("#update_bar_chart").on("click", function() {
- var attribute, sortItems, sorted_sample_names, x_scale;
+ $(".sort_by_value").on("click", function() {
+ console.log("sorting by value");
+ _this.sort_by = "value";
if (_this.attributes.length > 0) {
- attribute = $("#color_attribute").val();
+ _this.attribute = $("#color_attribute").val();
}
- if ($("#update_bar_chart").html() === 'Sort By Value') {
- $("#update_bar_chart").html('Sort By Name');
- 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);
- } else {
- $("#update_bar_chart").html('Sort By Value');
- _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);
+ return _this.rebuild_bar_graph(_this.sorted_samples());
+ });
+ $(".sort_by_name").on("click", function() {
+ console.log("sorting by name");
+ _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.get_attr_color_dict = function() {
- var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _ref, _results,
+ 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;
this.attr_color_dict = {};
- console.log("distinct_attr_vals:", this.distinct_attr_vals);
- _ref = this.distinct_attr_vals;
+ console.log("vals:", vals);
_results = [];
- for (key in _ref) {
- if (!__hasProp.call(_ref, key)) continue;
- distinct_vals = _ref[key];
+ for (key in vals) {
+ if (!__hasProp.call(vals, key)) continue;
+ distinct_vals = vals[key];
this_color_dict = {};
if (distinct_vals.length < 10) {
color = d3.scale.category10();
@@ -153,11 +151,11 @@
return true;
}
})) {
- color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 4]);
+ color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]);
for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) {
value = distinct_vals[i];
- console.log("color_range(value):", color_range(parseInt(value)));
- this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)));
+ console.log("color_range(value):", parseInt(color_range(value)));
+ this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0);
}
}
}
@@ -166,6 +164,18 @@
return _results;
};
+ Bar_Chart.prototype.convert_into_colors = function(values) {
+ var color_range, i, value, _i, _len, _results;
+ color_range = d3.scale.linear().domain([d3.min(values), d3.max(values)]).range([0, 255]);
+ _results = [];
+ for (i = _i = 0, _len = values.length; _i < _len; i = ++_i) {
+ value = values[i];
+ console.log("color_range(value):", color_range(parseInt(value)));
+ _results.push(this_color_dict[value] = d3.rgb(color_range(parseInt(value)), 0, 0));
+ }
+ return _results;
+ };
+
Bar_Chart.prototype.get_samples = function() {
var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1;
this.sample_names = (function() {
@@ -317,14 +327,58 @@
});
};
- Bar_Chart.prototype.color_by_trait = function() {
- console.log("Before load");
- $('#collections_holder').load('/collections/list #collections_list');
- $.colorbox({
- inline: true,
- href: "#collections_holder"
+ Bar_Chart.prototype.open_trait_selection = function() {
+ var _this = this;
+ return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', function() {
+ $.colorbox({
+ inline: true,
+ href: "#collections_holder"
+ });
+ return $('a.collection_name').attr('onClick', 'return false');
});
- return console.log("After load");
+ };
+
+ Bar_Chart.prototype.color_by_trait = function(trait_sample_data) {
+ var distinct_values, trimmed_samples,
+ _this = this;
+ console.log("BXD1:", trait_sample_data["BXD1"]);
+ console.log("trait_sample_data:", trait_sample_data);
+ trimmed_samples = this.trim_values(trait_sample_data);
+ distinct_values = {};
+ distinct_values["collection_trait"] = this.get_distinct_values(trimmed_samples);
+ this.get_attr_color_dict(distinct_values);
+ if ($("#update_bar_chart").html() === 'Sort By Name') {
+ return this.svg.selectAll(".bar").data(this.sorted_samples()).transition().duration(1000).style("fill", function(d) {
+ return _this.attr_color_dict["collection_trait"][trimmed_samples[d[0]]];
+ }).select("title").text(function(d) {
+ return d[1];
+ });
+ } else {
+ return this.svg.selectAll(".bar").data(this.samples).transition().duration(1000).style("fill", function(d) {
+ return _this.attr_color_dict["collection_trait"][trimmed_samples[d[0]]];
+ });
+ }
+ };
+
+ Bar_Chart.prototype.trim_values = function(trait_sample_data) {
+ var sample, trimmed_samples, _i, _len, _ref;
+ trimmed_samples = {};
+ _ref = this.sample_names;
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ sample = _ref[_i];
+ if (sample in trait_sample_data) {
+ trimmed_samples[sample] = trait_sample_data[sample];
+ }
+ }
+ console.log("trimmed_samples:", trimmed_samples);
+ return trimmed_samples;
+ };
+
+ Bar_Chart.prototype.get_distinct_values = function(samples) {
+ var distinct_values;
+ distinct_values = _.uniq(_.values(samples));
+ console.log("distinct_values:", distinct_values);
+ return distinct_values;
};
return Bar_Chart;
diff --git a/wqflask/wqflask/static/new/javascript/box_plot.coffee b/wqflask/wqflask/static/new/javascript/box_plot.coffee
index 562bd1dc..e9035456 100644
--- a/wqflask/wqflask/static/new/javascript/box_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/box_plot.coffee
@@ -5,46 +5,53 @@ class Box_Plot
@get_samples()
@margin = {top: 10, right: 50, bottom: 20, left: 50}
- @plot_width = 120 - @margin.left - @margin.right
+ @plot_width = 200 - @margin.left - @margin.right
@plot_height = 500 - @margin.top - @margin.bottom
@min = d3.min(@sample_vals)
- @max = d3.max(@sample_vals) * 1.1
+ @max = d3.max(@sample_vals)
@svg = @create_svg()
-
@enter_data()
-
+
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)
- @samples = _.zip(@sample_names, @sample_vals)
- create_svg: () -> d3.chart.box()
- .whiskers(@inter_quartile_range(1.5))
- .width(@plot_width)
- .height(@plot_height)
- .domain([@min, @max])
-
+ create_svg: () ->
+ svg = d3.box()
+ .whiskers(@inter_quartile_range(1.5))
+ .width(@plot_width)
+ .height(@plot_height)
+ .domain([@min, @max])
+ return svg
+
enter_data: () ->
d3.select("#box_plot").selectAll("svg")
- .data(@sample_vals)
+ .data([@sample_vals])
.enter().append("svg:svg")
.attr("class", "box")
.attr("width", @plot_width)
.attr("height", @plot_height)
+ .append("svg:g")
.call(@svg)
inter_quartile_range: (k) ->
return (d, i) =>
- q1 = d.quartiles[0],
- q3 = d.quartiles[2],
+ console.log("iqr d:", d)
+ q1 = d.quartiles[0]
+ q3 = d.quartiles[2]
inter_quartile_range = (q3 - q1) * k
- i = -1
+ console.log("iqr:", inter_quartile_range)
+ i = 0
j = d.length
- while (d[++i] < q1 - inter_quartile_range)
- while (d[--j] > q3 + inter_quartile_range)
+ console.log("d[-1]:", d[1])
+ console.log("q1 - iqr:", q1 - inter_quartile_range)
+ i++ while (d[i] < q1 - inter_quartile_range)
+ j-- while (d[j] > q3 + inter_quartile_range)
+ #while (d[++i] < q1 - inter_quartile_range
+ #while d[--j] > q3 + inter_quartile_range
+ console.log("[i, j]", [i, j])
return [i, j]
- \ No newline at end of file
+root.Box_Plot = Box_Plot \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/box_plot.js b/wqflask/wqflask/static/new/javascript/box_plot.js
new file mode 100644
index 00000000..2dd624e1
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/box_plot.js
@@ -0,0 +1,83 @@
+// Generated by CoffeeScript 1.6.1
+(function() {
+ var Box_Plot, root;
+
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+ Box_Plot = (function() {
+
+ function Box_Plot(sample_list, sample_group) {
+ this.sample_list = sample_list;
+ this.sample_group = sample_group;
+ this.get_samples();
+ this.margin = {
+ top: 10,
+ right: 50,
+ bottom: 20,
+ left: 50
+ };
+ this.plot_width = 200 - this.margin.left - this.margin.right;
+ this.plot_height = 500 - this.margin.top - this.margin.bottom;
+ this.min = d3.min(this.sample_vals);
+ this.max = d3.max(this.sample_vals);
+ this.svg = this.create_svg();
+ this.enter_data();
+ }
+
+ Box_Plot.prototype.get_samples = 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);
+ }
+ }
+ return _results;
+ }).call(this);
+ };
+
+ Box_Plot.prototype.create_svg = function() {
+ var svg;
+ svg = d3.box().whiskers(this.inter_quartile_range(1.5)).width(this.plot_width).height(this.plot_height).domain([this.min, this.max]);
+ return svg;
+ };
+
+ Box_Plot.prototype.enter_data = function() {
+ return d3.select("#box_plot").selectAll("svg").data([this.sample_vals]).enter().append("svg:svg").attr("class", "box").attr("width", this.plot_width).attr("height", this.plot_height).append("svg:g").call(this.svg);
+ };
+
+ Box_Plot.prototype.inter_quartile_range = function(k) {
+ var _this = this;
+ return function(d, i) {
+ var inter_quartile_range, j, q1, q3;
+ console.log("iqr d:", d);
+ q1 = d.quartiles[0];
+ q3 = d.quartiles[2];
+ inter_quartile_range = (q3 - q1) * k;
+ console.log("iqr:", inter_quartile_range);
+ i = 0;
+ j = d.length;
+ console.log("d[-1]:", d[1]);
+ console.log("q1 - iqr:", q1 - inter_quartile_range);
+ while (d[i] < q1 - inter_quartile_range) {
+ i++;
+ }
+ while (d[j] > q3 + inter_quartile_range) {
+ j--;
+ }
+ console.log("[i, j]", [i, j]);
+ return [i, j];
+ };
+ };
+
+ return Box_Plot;
+
+ })();
+
+ root.Box_Plot = Box_Plot;
+
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
new file mode 100644
index 00000000..db398809
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
@@ -0,0 +1,73 @@
+root = exports ? this
+
+console.log("before get_traits_from_collection")
+
+# Going to be used to hold collection list
+# So we can repopulate it when the back button is clicked
+collection_list = null
+this_trait_data = null
+
+collection_click = () ->
+ console.log("Clicking on:", $(this))
+ this_collection_url = $(this).find('.collection_name').prop("href")
+ this_collection_url += "&json"
+ console.log("this_collection_url", this_collection_url)
+ collection_list = $("#collections_holder").html()
+ $.ajax(
+ dataType: "json",
+ url: this_collection_url,
+ success: process_traits
+ )
+
+trait_click = () ->
+ console.log("Clicking on:", $(this))
+ trait = $(this).find('.trait').text()
+ dataset = $(this).find('.dataset').text()
+ this_trait_url = "/trait/get_sample_data?trait="+trait+"&dataset="+dataset
+ console.log("this_trait_url", this_trait_url)
+ $.ajax(
+ dataType: "json",
+ url: this_trait_url,
+ success: color_by_trait
+ )
+ $.colorbox.close()
+
+color_by_trait = (trait_sample_data, textStatus, jqXHR) ->
+ #trait_sample_data = trait_sample_data
+ #console.log('in color_by_trait:', trait_sample_data)
+ root.bar_chart.color_by_trait(trait_sample_data)
+
+process_traits = (trait_data, textStatus, jqXHR) ->
+ console.log('in process_traits with trait_data:', trait_data)
+
+ the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>"
+ the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>"
+
+ the_html += "<table class='table table-hover'>"
+ the_html += "<thead><tr><th>Record</th><th>Data Set</th><th>Description</th><th>Mean</th></tr></thead>"
+ the_html += "<tbody>"
+ for trait in trait_data
+ the_html += "<tr class='trait_line'><td class='trait'>#{ trait.name }</td>"
+ the_html += "<td class='dataset'>#{ trait.dataset }</td>"
+ the_html += "<td>#{ trait.description }</td>"
+ the_html += "<td>#{ trait.mean or '&nbsp;' }</td></tr>"
+ the_html += "</tbody>"
+ the_html += "</table>"
+
+ $("#collections_holder").html(the_html)
+ $('#collections_holder').colorbox.resize()
+
+back_to_collections = () ->
+ console.log("collection_list:", collection_list)
+ $("#collections_holder").html(collection_list)
+
+ $(document).on("click", ".collection_line", collection_click)
+ $('#collections_holder').colorbox.resize()
+
+$ ->
+ console.log("inside get_traits_from_collection")
+
+ $(document).on("click", ".collection_line", collection_click)
+ $(document).on("click", ".trait_line", trait_click)
+ $(document).on("click", "#back_to_collections", back_to_collections)
+
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
new file mode 100644
index 00000000..fac543f8
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -0,0 +1,82 @@
+// Generated by CoffeeScript 1.6.1
+(function() {
+ var back_to_collections, collection_click, collection_list, color_by_trait, process_traits, root, this_trait_data, trait_click;
+
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+ console.log("before get_traits_from_collection");
+
+ collection_list = null;
+
+ this_trait_data = null;
+
+ collection_click = function() {
+ var this_collection_url;
+ console.log("Clicking on:", $(this));
+ this_collection_url = $(this).find('.collection_name').prop("href");
+ this_collection_url += "&json";
+ console.log("this_collection_url", this_collection_url);
+ collection_list = $("#collections_holder").html();
+ return $.ajax({
+ dataType: "json",
+ url: this_collection_url,
+ success: process_traits
+ });
+ };
+
+ trait_click = function() {
+ var dataset, this_trait_url, trait;
+ console.log("Clicking on:", $(this));
+ trait = $(this).find('.trait').text();
+ dataset = $(this).find('.dataset').text();
+ this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset;
+ console.log("this_trait_url", this_trait_url);
+ return $.ajax({
+ dataType: "json",
+ url: this_trait_url,
+ success: color_by_trait
+ });
+ };
+
+ $.colorbox.close();
+
+ color_by_trait = function(trait_sample_data, textStatus, jqXHR) {
+ return root.bar_chart.color_by_trait(trait_sample_data);
+ };
+
+ process_traits = function(trait_data, textStatus, jqXHR) {
+ var the_html, trait, _i, _len;
+ console.log('in process_traits with trait_data:', trait_data);
+ the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>";
+ the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>";
+ the_html += "<table class='table table-hover'>";
+ the_html += "<thead><tr><th>Record</th><th>Data Set</th><th>Description</th><th>Mean</th></tr></thead>";
+ the_html += "<tbody>";
+ for (_i = 0, _len = trait_data.length; _i < _len; _i++) {
+ trait = trait_data[_i];
+ the_html += "<tr class='trait_line'><td class='trait'>" + trait.name + "</td>";
+ the_html += "<td class='dataset'>" + trait.dataset + "</td>";
+ the_html += "<td>" + trait.description + "</td>";
+ the_html += "<td>" + (trait.mean || '&nbsp;') + "</td></tr>";
+ }
+ the_html += "</tbody>";
+ the_html += "</table>";
+ $("#collections_holder").html(the_html);
+ return $('#collections_holder').colorbox.resize();
+ };
+
+ back_to_collections = function() {
+ console.log("collection_list:", collection_list);
+ $("#collections_holder").html(collection_list);
+ $(document).on("click", ".collection_line", collection_click);
+ return $('#collections_holder').colorbox.resize();
+ };
+
+ $(function() {
+ console.log("inside get_traits_from_collection");
+ $(document).on("click", ".collection_line", collection_click);
+ $(document).on("click", ".trait_line", trait_click);
+ return $(document).on("click", "#back_to_collections", back_to_collections);
+ });
+
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
new file mode 100644
index 00000000..81db186b
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
@@ -0,0 +1,297 @@
+$ ->
+
+ class Interval_Map
+ constructor: (@plot_height, @plot_width) ->
+ @qtl_results = js_data.qtl_results
+ console.log("qtl_results are:", @qtl_results)
+ @chromosomes = js_data.chromosomes
+
+ @total_length = 0
+
+ @max_chr = @get_max_chr()
+
+ @x_coords = []
+ @y_coords = []
+ @marker_names = []
+ console.time('Create coordinates')
+ @create_coordinates()
+ console.log("@x_coords: ", @x_coords)
+ console.log("@y_coords: ", @y_coords)
+ console.timeEnd('Create coordinates')
+ [@chr_lengths, @cumulative_chr_lengths] = @get_chr_lengths()
+
+ # Buffer to allow for the ticks/labels to be drawn
+ @x_buffer = @plot_width/30
+ @y_buffer = @plot_height/20
+
+ #@x_max = d3.max(@x_coords)
+ @x_max = @total_length
+ console.log("@x_max: ", @x_max)
+ console.log("@x_buffer: ", @x_buffer)
+ @y_max = d3.max(@y_coords) * 1.2
+
+ @svg = @create_svg()
+ @plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names)
+
+ @plot_height -= @y_buffer
+ @create_scales()
+ console.time('Create graph')
+ @create_graph()
+ console.timeEnd('Create graph')
+
+ get_max_chr: () ->
+ max_chr = 0
+ for result in @qtl_results
+ chr = parseInt(result.chr)
+ if not _.isNaN(chr)
+ if chr > max_chr
+ max_chr = chr
+ return max_chr
+
+ 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
+ #
+ ###
+
+ console.log("@chromosomes: ", @chromosomes)
+
+ cumulative_chr_lengths = []
+ chr_lengths = []
+ total_length = 0
+ for key of @chromosomes
+ this_length = @chromosomes[key]
+ 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.chr == "X"
+ chr_length = parseFloat(@chromosomes[20])
+ else
+ 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.chr != "1"
+ @total_length += parseFloat(chr_lengths[chr_lengths.length - 2])
+ @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")
+ .attr("class", "interval_map")
+ .attr("width", @plot_width+@x_buffer)
+ .attr("height", @plot_height+@y_buffer)
+
+ return svg
+
+ create_graph: () ->
+ @add_border()
+ @add_x_axis()
+ @add_y_axis()
+ @add_chr_lines()
+ @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()
+ .append("line")
+ .attr("y1", (d) =>
+ return d[0]
+ )
+ .attr("y2", (d) =>
+ return d[1]
+ )
+ .attr("x1", (d) =>
+ return d[2]
+ )
+ .attr("x2", (d) =>
+ 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
+ tick_vals.push(val)
+
+ for length, i in @cumulative_chr_lengths
+ if i == 0
+ continue
+ chr_ticks = []
+ tick_count = Math.floor(@chr_lengths[i]/25)
+ tick_val = parseInt(@cumulative_chr_lengths[i-1])
+ for tick in [0..(tick_count-1)]
+ tick_val += 25
+ chr_ticks.push(tick_val)
+ Array::push.apply tick_vals, chr_ticks
+
+ #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) =>
+ d3.format("d") #format as integer
+ if d < @cumulative_chr_lengths[0]
+ tick_val = d
+ else
+ next_chr_length = @cumulative_chr_lengths[next_chr]
+ if d > next_chr_length
+ next_chr += 1
+ tmp_tick_val = 25
+ tick_val = tmp_tick_val
+ else
+ tmp_tick_val += 25
+ tick_val = tmp_tick_val
+ return (tick_val)
+ )
+
+ @svg.append("g")
+ .attr("class", "x_axis")
+ .attr("transform", "translate(0," + @plot_height + ")")
+ .call(xAxis)
+ .selectAll("text")
+ .attr("text-anchor", "right")
+ .attr("dx", "-1.6em")
+ .attr("transform", (d) =>
+ return "translate(-12,0) rotate(-90)"
+ )
+ #.attr("dy", "-1.0em")
+
+
+ add_y_axis: () ->
+ yAxis = d3.svg.axis()
+ .scale(@y_scale)
+ .orient("left")
+ .ticks(5)
+
+ @svg.append("g")
+ .attr("class", "y_axis")
+ .attr("transform", "translate(" + @x_buffer + ",0)")
+ .call(yAxis)
+
+ add_chr_lines: () ->
+ @svg.selectAll("line")
+ .data(@cumulative_chr_lengths, (d) =>
+ return d
+ )
+ .enter()
+ .append("line")
+ .attr("y1", @y_buffer)
+ .attr("y2", @plot_height)
+ .attr("x1", @x_scale)
+ .attr("x2", @x_scale)
+ .style("stroke", "#ccc")
+
+ fill_chr_areas: () ->
+ @svg.selectAll("rect.chr_fill_area_1")
+ .data(_.zip(@chr_lengths, @cumulative_chr_lengths), (d) =>
+ return d
+ )
+ .enter()
+ .append("rect")
+ .attr("class", "chr_fill_area_1")
+ .attr("x", (d, i) =>
+ if i == 0
+ return @x_scale(0)
+ else
+ return @x_scale(@cumulative_chr_lengths[i-1])
+ )
+ .attr("y", @y_buffer)
+ .attr("width", (d) =>
+ return @x_scale(d[0])
+ )
+ .attr("height", @plot_height-@y_buffer)
+ .attr("fill", "white")
+
+ add_chr_labels: () ->
+ chr_names = []
+ for key of @chromosomes
+ chr_names.push(key)
+ chr_info = _.zip(chr_names, @chr_lengths, @cumulative_chr_lengths)
+ @svg.selectAll("text")
+ .data(chr_info, (d) =>
+ return d
+ )
+ .enter()
+ .append("text")
+ .text((d) =>
+ return d[0]
+ )
+ .attr("x", (d) =>
+ return @x_scale(d[2] - d[1]/2)
+ )
+ .attr("y", @plot_height * 0.1)
+ .attr("dx", "0em")
+ .attr("text-anchor", "middle")
+ .attr("font-family", "sans-serif")
+ .attr("font-size", "18px")
+ #.attr("fill", "grey")
+
+ connect_markers: () ->
+ @svg.selectAll("line")
+ .data(@plot_coordinates)
+ .enter()
+ .append("line")
+ .attr("x1", (d, i) =>
+ if i == 0
+ return @x_buffer
+ else
+ return parseFloat(@x_buffer) + ((parseFloat(@plot_width)-parseFloat(@x_buffer)) * @plot_coordinates[i-1][0]/parseFloat(@x_max))
+ )
+ .attr("y1", (d, i) =>
+ if i == 0
+ return @plot_height
+ else
+ return @plot_height - ((@plot_height-@y_buffer) * @plot_coordinates[i-1][1]/@y_max)
+ )
+ .attr("x2", (d) =>
+ return parseFloat(@x_buffer) + ((parseFloat(@plot_width)-parseFloat(@x_buffer)) * d[0]/parseFloat(@x_max))
+ )
+ .attr("y2", (d) =>
+ return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
+ )
+ .style("stroke", "black")
+
+ console.time('Create interval map')
+ console.log("TESTING")
+ new Interval_Map(600, 1200)
+ 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
new file mode 100644
index 00000000..3a2ce6d7
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.js
@@ -0,0 +1,273 @@
+// Generated by CoffeeScript 1.6.1
+(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 Interval_Map;
+ Interval_Map = (function() {
+
+ function Interval_Map(plot_height, plot_width) {
+ var _ref;
+ this.plot_height = plot_height;
+ this.plot_width = plot_width;
+ this.qtl_results = js_data.qtl_results;
+ console.log("qtl_results are:", this.qtl_results);
+ this.chromosomes = js_data.chromosomes;
+ this.total_length = 0;
+ this.max_chr = this.get_max_chr();
+ this.x_coords = [];
+ this.y_coords = [];
+ this.marker_names = [];
+ console.time('Create coordinates');
+ this.create_coordinates();
+ console.log("@x_coords: ", this.x_coords);
+ console.log("@y_coords: ", this.y_coords);
+ console.timeEnd('Create coordinates');
+ _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
+ this.x_buffer = this.plot_width / 30;
+ this.y_buffer = this.plot_height / 20;
+ this.x_max = this.total_length;
+ console.log("@x_max: ", this.x_max);
+ console.log("@x_buffer: ", this.x_buffer);
+ this.y_max = d3.max(this.y_coords) * 1.2;
+ this.svg = this.create_svg();
+ this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
+ this.plot_height -= this.y_buffer;
+ this.create_scales();
+ console.time('Create graph');
+ this.create_graph();
+ console.timeEnd('Create graph');
+ }
+
+ Interval_Map.prototype.get_max_chr = function() {
+ var chr, max_chr, result, _i, _len, _ref;
+ max_chr = 0;
+ _ref = this.qtl_results;
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ result = _ref[_i];
+ chr = parseInt(result.chr);
+ if (!_.isNaN(chr)) {
+ if (chr > max_chr) {
+ max_chr = chr;
+ }
+ }
+ }
+ return max_chr;
+ };
+
+ Interval_Map.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
+ #
+ */
+
+ var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
+ console.log("@chromosomes: ", this.chromosomes);
+ cumulative_chr_lengths = [];
+ chr_lengths = [];
+ total_length = 0;
+ for (key in this.chromosomes) {
+ this_length = this.chromosomes[key];
+ 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];
+ };
+
+ Interval_Map.prototype.create_coordinates = function() {
+ var chr_length, chr_lengths, chr_seen, result, _i, _len, _ref, _ref1;
+ chr_lengths = [];
+ chr_seen = [];
+ _ref = js_data.qtl_results;
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ result = _ref[_i];
+ if (result.chr === "X") {
+ chr_length = parseFloat(this.chromosomes[20]);
+ } else {
+ chr_length = parseFloat(this.chromosomes[result.chr]);
+ }
+ if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
+ chr_seen.push(result.chr);
+ chr_lengths.push(chr_length);
+ if (result.chr !== "1") {
+ this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
+ }
+ }
+ 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]);
+ };
+
+ Interval_Map.prototype.create_svg = function() {
+ var svg;
+ svg = d3.select("#interval_map").append("svg").attr("class", "interval_map").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer);
+ return svg;
+ };
+
+ Interval_Map.prototype.create_graph = function() {
+ this.add_border();
+ this.add_x_axis();
+ this.add_y_axis();
+ this.add_chr_lines();
+ this.fill_chr_areas();
+ this.add_chr_labels();
+ return this.connect_markers();
+ };
+
+ Interval_Map.prototype.add_border = function() {
+ var border_coords,
+ _this = this;
+ border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]];
+ return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", function(d) {
+ return d[0];
+ }).attr("y2", function(d) {
+ return d[1];
+ }).attr("x1", function(d) {
+ return d[2];
+ }).attr("x2", function(d) {
+ return d[3];
+ }).style("stroke", "#000");
+ };
+
+ Interval_Map.prototype.create_scales = function() {
+ this.x_scale = d3.scale.linear().domain([0, d3.max(this.x_coords)]).range([this.x_buffer, this.plot_width]);
+ return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
+ };
+
+ Interval_Map.prototype.create_x_axis_tick_values = function() {
+ var chr_ticks, i, length, tick, tick_count, tick_val, tick_vals, val, _i, _j, _k, _len, _ref, _ref1, _ref2;
+ tick_vals = [];
+ for (val = _i = 25, _ref = this.cumulative_chr_lengths[0]; 25 <= _ref ? _i <= _ref : _i >= _ref; val = 25 <= _ref ? ++_i : --_i) {
+ if (val % 25 === 0) {
+ tick_vals.push(val);
+ }
+ }
+ _ref1 = this.cumulative_chr_lengths;
+ for (i = _j = 0, _len = _ref1.length; _j < _len; i = ++_j) {
+ length = _ref1[i];
+ if (i === 0) {
+ continue;
+ }
+ chr_ticks = [];
+ tick_count = Math.floor(this.chr_lengths[i] / 25);
+ tick_val = parseInt(this.cumulative_chr_lengths[i - 1]);
+ for (tick = _k = 0, _ref2 = tick_count - 1; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; tick = 0 <= _ref2 ? ++_k : --_k) {
+ tick_val += 25;
+ chr_ticks.push(tick_val);
+ }
+ Array.prototype.push.apply(tick_vals, chr_ticks);
+ }
+ return tick_vals;
+ };
+
+ Interval_Map.prototype.add_x_axis = function() {
+ var next_chr, tmp_tick_val, xAxis,
+ _this = this;
+ xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").tickValues(this.create_x_axis_tick_values());
+ next_chr = 1;
+ tmp_tick_val = 0;
+ xAxis.tickFormat(function(d) {
+ var next_chr_length, tick_val;
+ d3.format("d");
+ if (d < _this.cumulative_chr_lengths[0]) {
+ tick_val = d;
+ } else {
+ next_chr_length = _this.cumulative_chr_lengths[next_chr];
+ if (d > next_chr_length) {
+ next_chr += 1;
+ tmp_tick_val = 25;
+ tick_val = tmp_tick_val;
+ } else {
+ tmp_tick_val += 25;
+ tick_val = tmp_tick_val;
+ }
+ }
+ return tick_val;
+ });
+ return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").attr("text-anchor", "right").attr("dx", "-1.6em").attr("transform", function(d) {
+ return "translate(-12,0) rotate(-90)";
+ });
+ };
+
+ Interval_Map.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").attr("transform", "translate(" + this.x_buffer + ",0)").call(yAxis);
+ };
+
+ Interval_Map.prototype.add_chr_lines = function() {
+ var _this = this;
+ return this.svg.selectAll("line").data(this.cumulative_chr_lengths, function(d) {
+ return d;
+ }).enter().append("line").attr("y1", this.y_buffer).attr("y2", this.plot_height).attr("x1", this.x_scale).attr("x2", this.x_scale).style("stroke", "#ccc");
+ };
+
+ Interval_Map.prototype.fill_chr_areas = function() {
+ var _this = this;
+ return this.svg.selectAll("rect.chr_fill_area_1").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) {
+ return d;
+ }).enter().append("rect").attr("class", "chr_fill_area_1").attr("x", function(d, i) {
+ if (i === 0) {
+ return _this.x_scale(0);
+ } else {
+ return _this.x_scale(_this.cumulative_chr_lengths[i - 1]);
+ }
+ }).attr("y", this.y_buffer).attr("width", function(d) {
+ return _this.x_scale(d[0]);
+ }).attr("height", this.plot_height - this.y_buffer).attr("fill", "white");
+ };
+
+ Interval_Map.prototype.add_chr_labels = function() {
+ var chr_info, chr_names, key,
+ _this = this;
+ chr_names = [];
+ for (key in this.chromosomes) {
+ chr_names.push(key);
+ }
+ chr_info = _.zip(chr_names, this.chr_lengths, this.cumulative_chr_lengths);
+ return this.svg.selectAll("text").data(chr_info, function(d) {
+ return d;
+ }).enter().append("text").text(function(d) {
+ return d[0];
+ }).attr("x", function(d) {
+ return _this.x_scale(d[2] - d[1] / 2);
+ }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px");
+ };
+
+ Interval_Map.prototype.connect_markers = function() {
+ var _this = this;
+ return this.svg.selectAll("line").data(this.plot_coordinates).enter().append("line").attr("x1", function(d, i) {
+ if (i === 0) {
+ return _this.x_buffer;
+ } else {
+ return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * _this.plot_coordinates[i - 1][0] / parseFloat(_this.x_max));
+ }
+ }).attr("y1", function(d, i) {
+ if (i === 0) {
+ return _this.plot_height;
+ } else {
+ return _this.plot_height - ((_this.plot_height - _this.y_buffer) * _this.plot_coordinates[i - 1][1] / _this.y_max);
+ }
+ }).attr("x2", function(d) {
+ return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max));
+ }).attr("y2", function(d) {
+ return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
+ }).style("stroke", "black");
+ };
+
+ return Interval_Map;
+
+ })();
+ console.time('Create interval map');
+ console.log("TESTING");
+ new Interval_Map(600, 1200);
+ 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.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 8bcca85d..1df033d6 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -1,3 +1,5 @@
+root = exports ? this
+
console.log("start_b")
# this is our isNumber, do not confuse with the underscore.js one
@@ -59,380 +61,13 @@ Stat_Table_Rows = [
]
$ ->
- class Bar_Chart
- constructor: (@sample_list, @sample_group) ->
- @get_samples()
- console.log("sample names:", @sample_names)
- if @sample_attr_vals.length > 0
- @get_distinct_attr_vals()
- @get_attr_color_dict()
-
- #Used to calculate the bottom margin so sample names aren't cut off
- longest_sample_name = d3.max(sample.length for sample in @sample_names)
-
- @margin = {top: 20, right: 20, bottom: longest_sample_name * 7, left: 40}
- @plot_width = @sample_vals.length * 15 - @margin.left - @margin.right
- @plot_height = 500 - @margin.top - @margin.bottom
-
- @x_buffer = @plot_width/20
- @y_buffer = @plot_height/20
-
- @y_min = d3.min(@sample_vals)
- @y_max = d3.max(@sample_vals) * 1.1
-
- @svg = @create_svg()
-
- @plot_height -= @y_buffer
- @create_scales()
- @create_graph()
-
- d3.select("#color_attribute").on("change", =>
- attribute = $("#color_attribute").val()
- if $("#update_bar_chart").html() == 'Sort By Name'
- @svg.selectAll(".bar")
- .data(@sorted_samples())
- .transition()
- .duration(1000)
- .style("fill", (d) =>
- if attribute == "None"
- return "steelblue"
- else
- return @attr_color_dict[attribute][d[2][attribute]]
- )
- .select("title")
- .text((d) =>
- return d[1]
- )
- else
- @svg.selectAll(".bar")
- .data(@samples)
- .transition()
- .duration(1000)
- .style("fill", (d) =>
- if attribute == "None"
- return "steelblue"
- else
- return @attr_color_dict[attribute][d[2][attribute]]
- )
- @add_legend(attribute, @distinct_attr_vals[attribute])
- )
-
-
- d3.select("#update_bar_chart").on("click", =>
- if @attributes.length > 0
- attribute = $("#color_attribute").val()
- if $("#update_bar_chart").html() == 'Sort By Value'
- $("#update_bar_chart").html('Sort By Name')
- 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)
- else
- $("#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)
- )
-
- d3.select("#color_by_trait").on("click", =>
- @color_by_trait()
- )
-
- get_attr_color_dict: () ->
- @attr_color_dict = {}
- console.log("distinct_attr_vals:", @distinct_attr_vals)
- for own key, distinct_vals of @distinct_attr_vals
- this_color_dict = {}
- if distinct_vals.length < 10
- color = d3.scale.category10()
- for value, i in distinct_vals
- this_color_dict[value] = color(i)
- else
- console.log("distinct_values:", distinct_vals)
- if _.every(distinct_vals, (d) =>
- if isNaN(d)
- return false
- else
- return true
- )
- color_range = d3.scale.linear()
- .domain([d3.min(distinct_vals),
- d3.max(distinct_vals)])
- .range([0,4])
- for value, i in distinct_vals
- console.log("color_range(value):", color_range(parseInt(value)))
- this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)))
- #this_color_dict[value] = "rgb(0, 0, " + color_range(parseInt(value)) + ")"
- @attr_color_dict[key] = this_color_dict
-
- 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)
- @sample_attr_vals = []
- if @attributes.length > 0
- for sample in @sample_list
- attr_vals = {}
- for attribute in @attributes
- attr_vals[attribute] = sample["extra_attributes"][attribute]
- @sample_attr_vals.push(attr_vals)
- @samples = _.zip(@sample_names, @sample_vals, @sample_attr_vals)
-
- get_distinct_attr_vals: () ->
- @distinct_attr_vals = {}
- for sample in @sample_attr_vals
- for attribute of sample
- if not @distinct_attr_vals[attribute]
- @distinct_attr_vals[attribute] = []
- if sample[attribute] not in @distinct_attr_vals[attribute]
- @distinct_attr_vals[attribute].push(sample[attribute])
- #console.log("distinct_attr_vals:", @distinct_attr_vals)
-
- create_svg: () ->
- svg = d3.select("#bar_chart")
- .append("svg")
- .attr("class", "bar_chart")
- .attr("width", @plot_width + @margin.left + @margin.right)
- .attr("height", @plot_height + @margin.top + @margin.bottom)
- .append("g")
- .attr("transform", "translate(" + @margin.left + "," + @margin.top + ")")
-
- return svg
-
- create_scales: () ->
- @x_scale = d3.scale.ordinal()
- .domain(@sample_names)
- .rangeBands([0, @plot_width], .1)
-
- @y_scale = d3.scale.linear()
- .domain([@y_min * 0.75, @y_max])
- .range([@plot_height, @y_buffer])
-
- create_graph: () ->
-
- #@add_border()
- @add_x_axis(@x_scale)
- @add_y_axis()
-
- @add_bars()
-
- add_x_axis: (scale) ->
- xAxis = d3.svg.axis()
- .scale(scale)
- .orient("bottom");
-
- @svg.append("g")
- .attr("class", "x axis")
- .attr("transform", "translate(0," + @plot_height + ")")
- .call(xAxis)
- .selectAll("text")
- .style("text-anchor", "end")
- .style("font-size", "12px")
- .attr("dx", "-.8em")
- .attr("dy", "-.3em")
- .attr("transform", (d) =>
- return "rotate(-90)"
- )
-
- add_y_axis: () ->
- yAxis = d3.svg.axis()
- .scale(@y_scale)
- .orient("left")
- .ticks(5)
-
- @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")
-
- add_bars: () ->
- @svg.selectAll(".bar")
- .data(@samples)
- .enter().append("rect")
- .style("fill", "steelblue")
- .attr("class", "bar")
- .attr("x", (d) =>
- return @x_scale(d[0])
- )
- .attr("width", @x_scale.rangeBand())
- .attr("y", (d) =>
- return @y_scale(d[1])
- )
- .attr("height", (d) =>
- return @plot_height - @y_scale(d[1])
- )
- .append("svg:title")
- .text((d) =>
- return d[1]
- )
-
- sorted_samples: () ->
- #if @sample_attr_vals.length > 0
- sample_list = _.zip(@sample_names, @sample_vals, @sample_attr_vals)
- #else
- # sample_list = _.zip(@sample_names, @sample_vals)
- sorted = _.sortBy(sample_list, (sample) =>
- return sample[1]
- )
- console.log("sorted:", sorted)
- return sorted
-
- add_legend: (attribute, distinct_vals) ->
- legend = @svg.append("g")
- .attr("class", "legend")
- .attr("height", 100)
- .attr("width", 100)
- .attr('transform', 'translate(-20,50)')
-
- legend_rect = legend.selectAll('rect')
- .data(distinct_vals)
- .enter()
- .append("rect")
- .attr("x", @plot_width - 65)
- .attr("width", 10)
- .attr("height", 10)
- .attr("y", (d, i) =>
- return i * 20
- )
- .style("fill", (d) =>
- console.log("TEST:", @attr_color_dict[attribute][d])
- return @attr_color_dict[attribute][d]
- )
-
- legend_text = legend.selectAll('text')
- .data(distinct_vals)
- .enter()
- .append("text")
- .attr("x", @plot_width - 52)
- .attr("y", (d, i) =>
- return i*20 + 9
- )
- .text((d) =>
- return d
- )
-
- color_by_trait: () ->
- $('#collections_holder').load('/collections/list #collections_list', =>
- $.colorbox(
- inline: true
- href: "#collections_holder"
- )
- )
-
- class Box_Plot
- constructor: (@sample_list, @sample_group) ->
- @get_samples()
-
- @margin = {top: 10, right: 50, bottom: 20, left: 50}
- @plot_width = 200 - @margin.left - @margin.right
- @plot_height = 500 - @margin.top - @margin.bottom
-
- @min = d3.min(@sample_vals)
- @max = d3.max(@sample_vals)
-
- @svg = @create_svg()
- @enter_data()
-
-
- get_samples: () ->
- @sample_vals = (sample.value for sample in @sample_list when sample.value != null)
-
- create_svg: () ->
- svg = d3.box()
- .whiskers(@inter_quartile_range(1.5))
- .width(@plot_width)
- .height(@plot_height)
- .domain([@min, @max])
- return svg
-
- enter_data: () ->
- d3.select("#box_plot").selectAll("svg")
- .data([@sample_vals])
- .enter().append("svg:svg")
- .attr("class", "box")
- .attr("width", @plot_width)
- .attr("height", @plot_height)
- .append("svg:g")
- .call(@svg)
-
- inter_quartile_range: (k) ->
- return (d, i) =>
- console.log("iqr d:", d)
- q1 = d.quartiles[0]
- q3 = d.quartiles[2]
- inter_quartile_range = (q3 - q1) * k
- console.log("iqr:", inter_quartile_range)
- i = 0
- j = d.length
- console.log("d[-1]:", d[1])
- console.log("q1 - iqr:", q1 - inter_quartile_range)
- i++ while (d[i] < q1 - inter_quartile_range)
- j-- while (d[j] > q3 + inter_quartile_range)
- #while (d[++i] < q1 - inter_quartile_range
- #while d[--j] > q3 + inter_quartile_range
- console.log("[i, j]", [i, j])
- return [i, j]
-
-
sample_lists = js_data.sample_lists
sample_group_types = js_data.sample_group_types
- new Bar_Chart(sample_lists[0])
+ $("#update_bar_chart.btn-group").button()
+ root.bar_chart = new Bar_Chart(sample_lists[0])
new Box_Plot(sample_lists[0])
-
$('.bar_chart_samples_group').change ->
$('#bar_chart').remove()
$('#bar_chart_container').append('<div id="bar_chart"></div>')
@@ -444,7 +79,8 @@ $ ->
else if group == "samples_all"
all_samples = sample_lists[0].concat sample_lists[1]
new Bar_Chart(all_samples)
-
+ #$(".btn-group").button()
+
$('.box_plot_samples_group').change ->
$('#box_plot').remove()
$('#box_plot_container').append('<div id="box_plot"></div>')
@@ -504,39 +140,6 @@ $ ->
console.log("Calling change_stats_value")
change_stats_value(sample_sets, category, row.vn, row.digits)
- edit_data_change = ->
- already_seen = {}
- sample_sets =
- samples_primary: new Stats([])
- samples_other: new Stats([])
- samples_all: new Stats([])
-
- console.log("at beginning:", sample_sets)
-
- tables = ['samples_primary', 'samples_other']
- for table in tables
- rows = $("#" + table).find('tr')
- for row in rows
- name = $(row).find('.edit_sample_sample_name').html()
- name = $.trim(name)
- real_value = $(row).find('.edit_sample_value').val()
- console.log("real_value:", real_value)
- checkbox = $(row).find(".edit_sample_checkbox")
- checked = $(checkbox).attr('checked')
-
- if checked and is_number(real_value) and real_value != ""
- console.log("in the iffy if")
- real_value = parseFloat(real_value)
-
- sample_sets[table].add_value(real_value)
- console.log("checking name of:", name)
- if not (name of already_seen)
- console.log("haven't seen")
- sample_sets['samples_all'].add_value(real_value)
- already_seen[name] = true
- console.log("towards end:", sample_sets)
- update_stat_values(sample_sets)
-
make_table = ->
header = "<thead><tr><th>&nbsp;</th>"
@@ -585,6 +188,38 @@ $ ->
processed += value
return processed
+ edit_data_change = ->
+ already_seen = {}
+ sample_sets =
+ samples_primary: new Stats([])
+ samples_other: new Stats([])
+ samples_all: new Stats([])
+
+ console.log("at beginning:", sample_sets)
+
+ tables = ['samples_primary', 'samples_other']
+ for table in tables
+ rows = $("#" + table).find('tr')
+ for row in rows
+ name = $(row).find('.edit_sample_sample_name').html()
+ name = $.trim(name)
+ real_value = $(row).find('.edit_sample_value').val()
+ console.log("real_value:", real_value)
+ checkbox = $(row).find(".edit_sample_checkbox")
+ checked = $(checkbox).attr('checked')
+
+ if checked and is_number(real_value) and real_value != ""
+ console.log("in the iffy if")
+ real_value = parseFloat(real_value)
+
+ sample_sets[table].add_value(real_value)
+ console.log("checking name of:", name)
+ if not (name of already_seen)
+ console.log("haven't seen")
+ sample_sets['samples_all'].add_value(real_value)
+ already_seen[name] = true
+ console.log("towards end:", sample_sets)
+ update_stat_values(sample_sets)
show_hide_outliers = ->
console.log("FOOBAR in beginning of show_hide_outliers")
@@ -613,7 +248,6 @@ $ ->
$('select[name=corr_method]').change(on_corr_method_change)
-
##End Calculate Correlations Code
##Populate Samples Attribute Values Code
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index b562bfe2..90fa8228 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1,10 +1,11 @@
// Generated by CoffeeScript 1.6.1
(function() {
- var Stat_Table_Rows, is_number,
+ var Stat_Table_Rows, is_number, root,
__hasProp = {}.hasOwnProperty,
- __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; },
__slice = [].slice;
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
console.log("start_b");
is_number = function(o) {
@@ -57,410 +58,11 @@
];
$(function() {
- var Bar_Chart, Box_Plot, block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
- Bar_Chart = (function() {
-
- function Bar_Chart(sample_list, sample_group) {
- var longest_sample_name, sample,
- _this = this;
- this.sample_list = sample_list;
- this.sample_group = sample_group;
- this.get_samples();
- console.log("sample names:", this.sample_names);
- if (this.sample_attr_vals.length > 0) {
- this.get_distinct_attr_vals();
- this.get_attr_color_dict();
- }
- longest_sample_name = d3.max((function() {
- var _i, _len, _ref, _results;
- _ref = this.sample_names;
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- _results.push(sample.length);
- }
- return _results;
- }).call(this));
- this.margin = {
- top: 20,
- right: 20,
- bottom: longest_sample_name * 7,
- left: 40
- };
- this.plot_width = this.sample_vals.length * 15 - 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.svg = this.create_svg();
- this.plot_height -= this.y_buffer;
- this.create_scales();
- this.create_graph();
- d3.select("#color_attribute").on("change", function() {
- var attribute;
- attribute = $("#color_attribute").val();
- if ($("#update_bar_chart").html() === 'Sort By Name') {
- _this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).style("fill", function(d) {
- if (attribute === "None") {
- return "steelblue";
- } else {
- return _this.attr_color_dict[attribute][d[2][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") {
- return "steelblue";
- } else {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- }
- });
- }
- return _this.add_legend(attribute, _this.distinct_attr_vals[attribute]);
- });
- d3.select("#update_bar_chart").on("click", function() {
- var attribute, sortItems, sorted_sample_names, x_scale;
- if (_this.attributes.length > 0) {
- attribute = $("#color_attribute").val();
- }
- if ($("#update_bar_chart").html() === 'Sort By Value') {
- $("#update_bar_chart").html('Sort By Name');
- 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);
- } else {
- $("#update_bar_chart").html('Sort By Value');
- _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);
- }
- });
- d3.select("#color_by_trait").on("click", function() {
- return _this.color_by_trait();
- });
- }
-
- Bar_Chart.prototype.get_attr_color_dict = function() {
- var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _ref, _results,
- _this = this;
- this.attr_color_dict = {};
- console.log("distinct_attr_vals:", this.distinct_attr_vals);
- _ref = this.distinct_attr_vals;
- _results = [];
- for (key in _ref) {
- if (!__hasProp.call(_ref, key)) continue;
- distinct_vals = _ref[key];
- this_color_dict = {};
- if (distinct_vals.length < 10) {
- color = d3.scale.category10();
- for (i = _i = 0, _len = distinct_vals.length; _i < _len; i = ++_i) {
- value = distinct_vals[i];
- this_color_dict[value] = color(i);
- }
- } else {
- console.log("distinct_values:", distinct_vals);
- if (_.every(distinct_vals, function(d) {
- if (isNaN(d)) {
- return false;
- } else {
- return true;
- }
- })) {
- color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 4]);
- for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) {
- value = distinct_vals[i];
- console.log("color_range(value):", color_range(parseInt(value)));
- this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)));
- }
- }
- }
- _results.push(this.attr_color_dict[key] = this_color_dict);
- }
- return _results;
- };
-
- Bar_Chart.prototype.get_samples = function() {
- var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1;
- this.sample_names = (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.name);
- }
- }
- return _results;
- }).call(this);
- 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);
- }
- }
- return _results;
- }).call(this);
- 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:", this.attributes);
- this.sample_attr_vals = [];
- if (this.attributes.length > 0) {
- _ref = this.sample_list;
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- attr_vals = {};
- _ref1 = this.attributes;
- for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
- attribute = _ref1[_j];
- attr_vals[attribute] = sample["extra_attributes"][attribute];
- }
- this.sample_attr_vals.push(attr_vals);
- }
- }
- return this.samples = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
- };
-
- Bar_Chart.prototype.get_distinct_attr_vals = function() {
- var attribute, sample, _i, _len, _ref, _results;
- this.distinct_attr_vals = {};
- _ref = this.sample_attr_vals;
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- _results.push((function() {
- var _ref1, _results1;
- _results1 = [];
- for (attribute in sample) {
- if (!this.distinct_attr_vals[attribute]) {
- this.distinct_attr_vals[attribute] = [];
- }
- if (_ref1 = sample[attribute], __indexOf.call(this.distinct_attr_vals[attribute], _ref1) < 0) {
- _results1.push(this.distinct_attr_vals[attribute].push(sample[attribute]));
- } else {
- _results1.push(void 0);
- }
- }
- return _results1;
- }).call(this));
- }
- return _results;
- };
-
- Bar_Chart.prototype.create_svg = function() {
- var svg;
- svg = d3.select("#bar_chart").append("svg").attr("class", "bar_chart").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;
- };
-
- Bar_Chart.prototype.create_scales = function() {
- 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]);
- };
-
- Bar_Chart.prototype.create_graph = function() {
- this.add_x_axis(this.x_scale);
- this.add_y_axis();
- return this.add_bars();
- };
-
- Bar_Chart.prototype.add_x_axis = function(scale) {
- var xAxis,
- _this = this;
- xAxis = d3.svg.axis().scale(scale).orient("bottom");
- return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").style("text-anchor", "end").style("font-size", "12px").attr("dx", "-.8em").attr("dy", "-.3em").attr("transform", function(d) {
- return "rotate(-90)";
- });
- };
-
- Bar_Chart.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");
- };
-
- Bar_Chart.prototype.add_bars = function() {
- var _this = this;
- return this.svg.selectAll(".bar").data(this.samples).enter().append("rect").style("fill", "steelblue").attr("class", "bar").attr("x", function(d) {
- return _this.x_scale(d[0]);
- }).attr("width", this.x_scale.rangeBand()).attr("y", function(d) {
- return _this.y_scale(d[1]);
- }).attr("height", function(d) {
- return _this.plot_height - _this.y_scale(d[1]);
- }).append("svg:title").text(function(d) {
- return d[1];
- });
- };
-
- Bar_Chart.prototype.sorted_samples = function() {
- var sample_list, sorted,
- _this = this;
- sample_list = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
- sorted = _.sortBy(sample_list, function(sample) {
- return sample[1];
- });
- console.log("sorted:", sorted);
- return sorted;
- };
-
- Bar_Chart.prototype.add_legend = function(attribute, distinct_vals) {
- var legend, legend_rect, legend_text,
- _this = this;
- legend = this.svg.append("g").attr("class", "legend").attr("height", 100).attr("width", 100).attr('transform', 'translate(-20,50)');
- legend_rect = legend.selectAll('rect').data(distinct_vals).enter().append("rect").attr("x", this.plot_width - 65).attr("width", 10).attr("height", 10).attr("y", function(d, i) {
- return i * 20;
- }).style("fill", function(d) {
- console.log("TEST:", _this.attr_color_dict[attribute][d]);
- return _this.attr_color_dict[attribute][d];
- });
- return legend_text = legend.selectAll('text').data(distinct_vals).enter().append("text").attr("x", this.plot_width - 52).attr("y", function(d, i) {
- return i * 20 + 9;
- }).text(function(d) {
- return d;
- });
- };
-
- Bar_Chart.prototype.color_by_trait = function() {
- var _this = this;
- return $('#collections_holder').load('/collections/list #collections_list', function() {
- return $.colorbox({
- inline: true,
- href: "#collections_holder"
- });
- });
- };
-
- return Bar_Chart;
-
- })();
- Box_Plot = (function() {
-
- function Box_Plot(sample_list, sample_group) {
- this.sample_list = sample_list;
- this.sample_group = sample_group;
- this.get_samples();
- this.margin = {
- top: 10,
- right: 50,
- bottom: 20,
- left: 50
- };
- this.plot_width = 200 - this.margin.left - this.margin.right;
- this.plot_height = 500 - this.margin.top - this.margin.bottom;
- this.min = d3.min(this.sample_vals);
- this.max = d3.max(this.sample_vals);
- this.svg = this.create_svg();
- this.enter_data();
- }
-
- Box_Plot.prototype.get_samples = 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);
- }
- }
- return _results;
- }).call(this);
- };
-
- Box_Plot.prototype.create_svg = function() {
- var svg;
- svg = d3.box().whiskers(this.inter_quartile_range(1.5)).width(this.plot_width).height(this.plot_height).domain([this.min, this.max]);
- return svg;
- };
-
- Box_Plot.prototype.enter_data = function() {
- return d3.select("#box_plot").selectAll("svg").data([this.sample_vals]).enter().append("svg:svg").attr("class", "box").attr("width", this.plot_width).attr("height", this.plot_height).append("svg:g").call(this.svg);
- };
-
- Box_Plot.prototype.inter_quartile_range = function(k) {
- var _this = this;
- return function(d, i) {
- var inter_quartile_range, j, q1, q3;
- console.log("iqr d:", d);
- q1 = d.quartiles[0];
- q3 = d.quartiles[2];
- inter_quartile_range = (q3 - q1) * k;
- console.log("iqr:", inter_quartile_range);
- i = 0;
- j = d.length;
- console.log("d[-1]:", d[1]);
- console.log("q1 - iqr:", q1 - inter_quartile_range);
- while (d[i] < q1 - inter_quartile_range) {
- i++;
- }
- while (d[j] > q3 + inter_quartile_range) {
- j--;
- }
- console.log("[i, j]", [i, j]);
- return [i, j];
- };
- };
-
- return Box_Plot;
-
- })();
+ var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
sample_lists = js_data.sample_lists;
sample_group_types = js_data.sample_group_types;
- new Bar_Chart(sample_lists[0]);
+ $("#update_bar_chart.btn-group").button();
+ root.bar_chart = new Bar_Chart(sample_lists[0]);
new Box_Plot(sample_lists[0]);
$('.bar_chart_samples_group').change(function() {
var all_samples, group;
@@ -546,43 +148,6 @@
}
return _results;
};
- edit_data_change = function() {
- var already_seen, checkbox, checked, name, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
- already_seen = {};
- sample_sets = {
- samples_primary: new Stats([]),
- samples_other: new Stats([]),
- samples_all: new Stats([])
- };
- console.log("at beginning:", sample_sets);
- tables = ['samples_primary', 'samples_other'];
- for (_i = 0, _len = tables.length; _i < _len; _i++) {
- table = tables[_i];
- rows = $("#" + table).find('tr');
- for (_j = 0, _len1 = rows.length; _j < _len1; _j++) {
- row = rows[_j];
- name = $(row).find('.edit_sample_sample_name').html();
- name = $.trim(name);
- real_value = $(row).find('.edit_sample_value').val();
- console.log("real_value:", real_value);
- checkbox = $(row).find(".edit_sample_checkbox");
- checked = $(checkbox).attr('checked');
- if (checked && is_number(real_value) && real_value !== "") {
- console.log("in the iffy if");
- real_value = parseFloat(real_value);
- sample_sets[table].add_value(real_value);
- console.log("checking name of:", name);
- if (!(name in already_seen)) {
- console.log("haven't seen");
- sample_sets['samples_all'].add_value(real_value);
- already_seen[name] = true;
- }
- }
- }
- }
- console.log("towards end:", sample_sets);
- return update_stat_values(sample_sets);
- };
make_table = function() {
var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
header = "<thead><tr><th>&nbsp;</th>";
@@ -645,6 +210,43 @@
}
return processed;
};
+ edit_data_change = function() {
+ var already_seen, checkbox, checked, name, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
+ already_seen = {};
+ sample_sets = {
+ samples_primary: new Stats([]),
+ samples_other: new Stats([]),
+ samples_all: new Stats([])
+ };
+ console.log("at beginning:", sample_sets);
+ tables = ['samples_primary', 'samples_other'];
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ rows = $("#" + table).find('tr');
+ for (_j = 0, _len1 = rows.length; _j < _len1; _j++) {
+ row = rows[_j];
+ name = $(row).find('.edit_sample_sample_name').html();
+ name = $.trim(name);
+ real_value = $(row).find('.edit_sample_value').val();
+ console.log("real_value:", real_value);
+ checkbox = $(row).find(".edit_sample_checkbox");
+ checked = $(checkbox).attr('checked');
+ if (checked && is_number(real_value) && real_value !== "") {
+ console.log("in the iffy if");
+ real_value = parseFloat(real_value);
+ sample_sets[table].add_value(real_value);
+ console.log("checking name of:", name);
+ if (!(name in already_seen)) {
+ console.log("haven't seen");
+ sample_sets['samples_all'].add_value(real_value);
+ already_seen[name] = true;
+ }
+ }
+ }
+ }
+ console.log("towards end:", sample_sets);
+ return update_stat_values(sample_sets);
+ };
show_hide_outliers = function() {
var label;
console.log("FOOBAR in beginning of show_hide_outliers");
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 3c995441..df9bfc9d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -52,6 +52,33 @@ $ ->
)
return false
+ $("#interval_mapping_compute").click(() =>
+ console.log("In interval mapping")
+ $("#progress_bar_container").modal()
+ url = "/interval_mapping"
+ form_data = $('#trait_data_form').serialize()
+ console.log("form_data is:", 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
+ )
+
$('#suggestive').hide()
$('input[name=display_all]').change(() =>
@@ -92,8 +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 b309b167..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;
@@ -62,6 +62,34 @@
});
return false;
};
+ $("#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();
+ console.log("form_data is:", form_data);
+ $.ajax({
+ type: "POST",
+ url: url,
+ data: form_data,
+ error: function(xhr, ajaxOptions, thrownError) {
+ alert("Sorry, an error occurred");
+ console.log(xhr);
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ return $("body").html("We got an error.");
+ },
+ success: function(data) {
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ return $("body").html(data);
+ }
+ });
+ console.log("settingInterval");
+ _this.my_timer = setInterval(get_progress, 1000);
+ return false;
+ });
$('#suggestive').hide();
$('input[name=display_all]').change(function() {
console.log("check");
@@ -101,7 +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/static/new/packages/DataTables/js/dataTables.scientific.js b/wqflask/wqflask/static/new/packages/DataTables/js/dataTables.scientific.js
new file mode 100644
index 00000000..82c55fda
--- /dev/null
+++ b/wqflask/wqflask/static/new/packages/DataTables/js/dataTables.scientific.js
@@ -0,0 +1,13 @@
+jQuery.extend( jQuery.fn.dataTableExt.oSort, {
+ "scientific-pre": function ( a ) {
+ return parseFloat(a);
+ },
+
+ "scientific-asc": function ( a, b ) {
+ return ((a < b) ? -1 : ((a > b) ? 1 : 0));
+ },
+
+ "scientific-desc": function ( a, b ) {
+ return ((a < b) ? 1 : ((a > b) ? -1 : 0));
+ }
+} ); \ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ea6db646..9b98c955 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -198,7 +198,7 @@
<!--</div>-->
</div>
- <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
<script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
<script>
//http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index dce7d41d..354723d0 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -5,6 +5,7 @@
{{ header("Your Collections",
'You have {}.'.format(numify(user_collections|count, "collection", "collections"))) }}
+
<div class="container">
<div class="page-header">
<h1>Collections owned by {{ g.user_session.user_ob.full_name }}</h1>
@@ -23,8 +24,8 @@
<tbody>
{% for uc in user_collections %}
- <tr>
- <td><a href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
+ <tr class="collection_line">
+ <td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
<td>{{ timeago(uc.created_timestamp.isoformat() + "Z") }}</td>
<td>{{ timeago(uc.changed_timestamp.isoformat() + "Z") }}</td>
<td>{{ uc.num_members }}</td>
@@ -33,6 +34,10 @@
</tbody>
</table>
+ {# if "color_by_trait" in params #}
+<!-- <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>-->
+ {# endif #}
+
</div>
</div>
@@ -41,10 +46,8 @@
{% endblock %}
{% block js %}
-
<script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
<script>
$('body').timeago();
</script>
-
{% endblock %}
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
new file mode 100644
index 00000000..e4e08388
--- /dev/null
+++ b/wqflask/wqflask/templates/interval_mapping.html
@@ -0,0 +1,107 @@
+{% extends "base.html" %}
+{% block title %}Interval Mapping{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+{% endblock %}
+{% block content %} <!-- Start of body -->
+
+ {{ header("Mapping",
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+
+ <div class="container">
+ <div>
+ <h2>
+ Whole Genome Mapping
+ </h2>
+ </div>
+ <div id="interval_map" class="interval_map">
+
+ </div>
+ <div>
+ <h2>
+ Results
+ </h2>
+ </div>
+ <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <td>Index</td>
+ <td>LRS Score</td>
+ {% if method == "qtl_reaper" %}
+ <td>Additive Effect</td>
+ {% endif %}
+ <td>Chr</td>
+ <td>Mb</td>
+ <td>Locus</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for marker in qtl_results %}
+ <tr>
+ <td>{{ loop.index }}</td>
+ <td>{{ marker.lrs_value|float }}</td>
+ {% if method == "qtl_reaper" %}
+ <td>{{ marker.additive|float }}</td>
+ {% endif %}
+ <td>{{ marker.chr|int }}</td>
+ <td>{{ marker.Mb|float }}</td>
+ <td>{{ marker.name }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+
+ </div>
+
+ <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script>
+ js_data = {{ js_data | safe }}
+ </script>
+
+ <!--[if lt IE 9]>
+<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
+ <![endif]-->
+ <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/interval_mapping.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+
+ <script type="text/javascript" charset="utf-8">
+ $(document).ready( function () {
+ console.time("Creating table");
+ $('#qtl_results').dataTable( {
+ //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+ "sDom": "lTftipr",
+ "oTableTools": {
+ "aButtons": [
+ "copy",
+ "print",
+ {
+ "sExtends": "collection",
+ "sButtonText": 'Save <span class="caret" />',
+ "aButtons": [ "csv", "xls", "pdf" ]
+ }
+ ],
+ "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+ },
+ "iDisplayLength": 50,
+ "bLengthChange": true,
+ "bDeferRender": true,
+ "bSortClasses": false
+ } );
+ console.timeEnd("Creating table");
+ });
+ </script>
+{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 8a19e07b..86891bb0 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -2,6 +2,7 @@
{% block title %}Trait Data and Analysis{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
@@ -55,8 +56,11 @@
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
<script type="text/javascript" src="/static/new/javascript/box.js"></script>
+ <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
<script type="text/javascript" src="/static/new/javascript/bar_chart.js"></script>
- <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
+ <script type="text/javascript" src="/static/new/javascript/box_plot.js"></script>
+
<script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
+ <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
<script type="text/javascript" src="/static/new/javascript/validation.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c2d5211f..58ee8982 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -17,9 +17,20 @@
<div class="tab-content">
<div class="tab-pane active" id="interval_mapping">
<div class="control-group">
+ <label for="mapping_method" class="control-label">Mapping Method</label>
+ <div class="controls" id="mapping_method_choice">
+ <select name="mapping_method">
+ <option value="qtl_reaper">H&K Regression</option>
+ <option value="pylmm">Linear Mixed</option>
+ </select>
+ </div>
+ </div>
+
+ <div class="control-group">
<label for="chromosome" class="control-label">Chromosome</label>
<div class="controls">
<select name="chromosome">
+ <option value="-1">All</option>
{% for name, value in dataset.species.chromosomes.chromosomes.items() %}
<option value="{{ value }}">{{ name }}</option>
{% endfor %}
@@ -27,14 +38,14 @@
</div>
</div>
- <div class="control-group">
+ <div class="control-group mapping_method_fields">
<label for="mapping_permutations" class="control-label">Permutations (n)</label>
<div class="controls">
- <input name="num_perm1" value="2000" type="text" />
+ <input name="num_permutations" value="2000" type="text" />
</div>
</div>
- <div class="control-group">
+ <div class="control-group mapping_method_fields">
<label for="mapping_bootstraps" class="control-label"
title="Bootstrapping Resamples">Bootstrap (n)</label>
<div class="controls">
@@ -43,7 +54,7 @@
</div>
- <div class="control-group">
+ <div class="control-group mapping_method_fields">
<label class="control-label"><b>Composite Mapping</b></label>
<div class="controls" id="use_composite_choice">
<label class="radio inline">
@@ -85,7 +96,8 @@
<div class="control-group">
<div class="controls">
- <button class="btn btn-inverse submit_special"
+ <button id="interval_mapping_compute"
+ class="btn btn-inverse submit_special"
data-url="/interval_mapping"
title="Compute Interval Mapping">
<i class="icon-ok-circle icon-white"></i> Compute
@@ -116,12 +128,12 @@
</div>
</div>
- <div class="control-group">
+<!-- <div class="control-group">
<label for="marker_reg_permutations" class="control-label">Permutations (n)</label>
<div class="controls">
<input name="num_perm" value="2000" type="text" />
</div>
- </div>
+ </div> -->
<div class="control-group">
<div class="controls">
diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html
index 6385089b..6d6b1d24 100644
--- a/wqflask/wqflask/templates/show_trait_statistics_new.html
+++ b/wqflask/wqflask/templates/show_trait_statistics_new.html
@@ -30,9 +30,23 @@
{% endfor %}
</select>
</div>
- {% endif %}
- <button type="button" id="update_bar_chart">Sort By Value</button>
- <button type="button" id="color_by_trait">Color by Trait</button>
+ {% endif %}
+ <div id="update_bar_chart" class="btn-group">
+ <button type="button" class="btn btn-default sort_by_name" value="name">
+ <i class="icon-resize-horizontal"></i> Sort By Name
+ </button>
+ <button type="button" class="btn btn-default sort_by_value" value="value">
+ <i class="icon-signal"></i> Sort By Value
+ </button>
+ </div>
+<!-- <button type="button" class="btn" id="update_bar_chart">
+ <i class="icon-resize-vertical"></i> Sort By Value
+ </button>-->
+ <div class="btn-group">
+ <button type="button" class="btn" id="color_by_trait">
+ <i class="icon-tint"></i> Color by Trait
+ </button>
+ </div>
<div id="bar_chart_container">
<div id="bar_chart"></div>
</div>
@@ -56,4 +70,5 @@
<div id="collections_holder_wrapper" style="display:none;">
<div id="collections_holder"></div>
</div>
+
</div> \ No newline at end of file
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 768415b5..1d0d9846 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -49,7 +49,8 @@ from utility import Bunch, Struct
from base.data_set import create_datasets_list
-
+THREE_DAYS = 60 * 60 * 24 * 3
+#THREE_DAYS = 45
def timestamp():
return datetime.datetime.utcnow().isoformat()
@@ -74,6 +75,27 @@ class UserSession(object):
print("self.redis_key is:", self.redis_key)
self.session_id = session_id
self.record = Redis.hgetall(self.redis_key)
+
+
+ if not self.record:
+ # This will occur, for example, when the browser has been left open over a long
+ # weekend and the site hasn't been visited by the user
+ self.logged_in = False
+
+ ########### Grrr...this won't work because of the way flask handles cookies
+ # Delete the cookie
+ #response = make_response(redirect(url_for('login')))
+ #response.set_cookie(self.cookie_name, '', expires=0)
+ #flash(
+ # "Due to inactivity your session has expired. If you'd like please login again.")
+ #return response
+ return
+
+ if Redis.ttl(self.redis_key) < THREE_DAYS:
+ # (Almost) everytime the user does something we extend the session_id in Redis...
+ print("Extending ttl...")
+ Redis.expire(self.redis_key, THREE_DAYS)
+
print("record is:", self.record)
self.logged_in = True
@@ -225,8 +247,8 @@ class VerificationEmail(object):
)
Redis.set(key, data)
- two_days = 60 * 60 * 24 * 2
- Redis.expire(key, two_days)
+ #two_days = 60 * 60 * 24 * 2
+ Redis.expire(key, THREE_DAYS)
to = user.email_address
subject = self.subject
body = render_template(self.template_name,
@@ -415,7 +437,7 @@ class LoginUser(object):
if self.remember_me:
expire_time = self.remember_time
else:
- expire_time = 60 * 60 * 24 * 2 # two days
+ expire_time = THREE_DAYS
Redis.expire(key, expire_time)
db_session.add(login_rec)
db_session.commit()
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b2f08ca0..828199c5 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -32,7 +32,7 @@ from base.data_set import create_datasets_list
from wqflask.show_trait import show_trait
from wqflask.show_trait import export_trait_data
from wqflask.marker_regression import marker_regression
-#from wqflask.interval_mapping import interval_mapping
+from wqflask.interval_mapping import interval_mapping
from wqflask.correlation import show_corr_results
from wqflask.correlation import corr_scatter_plot
from utility import temp_data
@@ -213,7 +213,7 @@ def marker_regression_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- version = "v14"
+ version = "v1"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
print("key is:", pf(key))
with Bench("Loading cache"):
@@ -237,8 +237,10 @@ def marker_regression_page():
result = template_vars.__dict__
- #for item in template_vars.__dict__.keys():
- # print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
+ print("DATASET:", pf(result['dataset']))
+
+ for item in template_vars.__dict__.keys():
+ print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
#causeerror
Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
@@ -256,7 +258,12 @@ def interval_mapping_page():
wanted = (
'trait_id',
'dataset',
- 'suggestive'
+ 'mapping_method',
+ 'chromosome',
+ 'num_permutations',
+ 'do_bootstraps',
+ 'default_control_locus',
+ 'control_locus'
)
start_vars = {}
@@ -264,7 +271,7 @@ def interval_mapping_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- version = "v1"
+ version = "v7"
key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
print("key is:", pf(key))
with Bench("Loading cache"):
@@ -284,6 +291,9 @@ def interval_mapping_page():
result = template_vars.__dict__
+ for item in template_vars.__dict__.keys():
+ print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
+
#causeerror
Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60*60)
@@ -308,10 +318,10 @@ def corr_scatter_plot_page():
indent=" ")
return render_template("corr_scatter_plot.html", **template_vars.__dict__)
-@app.route("/int_mapping", methods=('POST',))
-def interval_mapping_page():
- template_vars = interval_mapping.IntervalMapping(request.args)
- return render_template("interval_mapping.html", **template_vars.__dict__)
+#@app.route("/int_mapping", methods=('POST',))
+#def interval_mapping_page():
+# template_vars = interval_mapping.IntervalMapping(request.args)
+# return render_template("interval_mapping.html", **template_vars.__dict__)
# Todo: Can we simplify this? -Sam
def sharing_info_page():