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-rw-r--r--misc/gn_installation_notes.txt6
-rw-r--r--misc/notes.txt3
-rwxr-xr-xwqflask/base/data_set.py1
-rwxr-xr-xwqflask/base/trait.py6
-rw-r--r--wqflask/other_config/nginx_conf/penguin.conf2
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py15
-rwxr-xr-x[-rw-r--r--]wqflask/wqflask/interval_mapping/interval_mapping.py70
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py2
-rw-r--r--wqflask/wqflask/static/new/css/bar_chart.css14
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.coffee264
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js271
-rw-r--r--wqflask/wqflask/templates/correlation_page.html119
-rw-r--r--wqflask/wqflask/templates/quick_search.html7
-rw-r--r--wqflask/wqflask/templates/search_result_page.html3
-rw-r--r--wqflask/wqflask/templates/show_trait.html3
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics_new.html29
-rw-r--r--wqflask/wqflask/views.py44
17 files changed, 755 insertions, 104 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
index a73e7d4f..584080f7 100644
--- a/misc/gn_installation_notes.txt
+++ b/misc/gn_installation_notes.txt
@@ -304,6 +304,12 @@ sudo apt-get install colordiff
==========================================
+Install NTP (network time protocol)
+
+sudo apt-get install ntp
+
+==========================================
+
To get server running:
!If having seemingly inexplicable problems with imports, make sure I've started the environment!
diff --git a/misc/notes.txt b/misc/notes.txt
index 91a0e67c..f6a2bb33 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -90,6 +90,9 @@ Reload web server:
Run server:
python runserver.py
+Run sendmail.py
+python send_mail.py
+
===========================================
UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index f25e7974..cd8c1ac1 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -224,6 +224,7 @@ class DatasetGroup(object):
"""
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
+ print("dataset name:", dataset.name)
self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
if self.name == 'BXD300':
self.name = "BXD"
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index aea1f9a9..731f99eb 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -387,6 +387,7 @@ class GeneralTrait(object):
#trait_qtl = self.cursor.fetchone()
if trait_qtl:
self.locus, self.lrs, self.pvalue, self.mean = trait_qtl
+ print("self.locus:", self.locus)
if self.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
@@ -395,8 +396,9 @@ class GeneralTrait(object):
Geno.SpeciesId = Species.Id
""".format(self.dataset.group.species, self.locus)
result = g.db.execute(query).fetchone()
- self.locus_chr = result[0]
- self.locus_mb = result[1]
+ if result:
+ self.locus_chr = result[0]
+ self.locus_mb = result[1]
else:
self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = ""
diff --git a/wqflask/other_config/nginx_conf/penguin.conf b/wqflask/other_config/nginx_conf/penguin.conf
index 822556d3..5c380da8 100644
--- a/wqflask/other_config/nginx_conf/penguin.conf
+++ b/wqflask/other_config/nginx_conf/penguin.conf
@@ -2,7 +2,7 @@ server {
# Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
listen 80;
- server_name penguin.uthsc.edu;
+ server_name gn2python.genenetwork.org;
access_log /var/log/nginx/access.log;
error_log /var/log/nginx/error.log;
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 8f23165c..0b66bc61 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -102,6 +102,7 @@ class CorrelationResults(object):
self.sample_data = {}
self.corr_type = start_vars['corr_type']
self.corr_method = start_vars['corr_sample_method']
+ self.get_formatted_corr_type()
self.return_number = 50
#The two if statements below append samples to the sample list based upon whether the user
@@ -239,6 +240,20 @@ class CorrelationResults(object):
############################################################################################################################################
+ def get_formatted_corr_type(self):
+ self.formatted_corr_type = ""
+ if self.corr_type == "lit":
+ self.formatted_corr_type += "Literature Correlation "
+ elif self.corr_type == "tissue":
+ self.formatted_corr_type += "Tissue Correlation "
+ elif self.corr_type == "sample":
+ self.formatted_corr_type += "Genetic Correlation "
+
+ if self.corr_method == "pearson":
+ self.formatted_corr_type += "(Pearson's r)"
+ elif self.corr_method == "spearman":
+ self.formatted_corr_type += "(Spearman's rho)"
+
def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1):
"""Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each"""
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 5d660224..aca99cbe 100644..100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -89,26 +89,56 @@ class IntervalMapping(object):
samples, values, variances = self.trait.export_informative()
if self.control_locus:
if self.weighted_regression:
- qtl_result = self.dataset.genotype.regression(strains = samples,
+ self.qtl_results = self.dataset.genotype.regression(strains = samples,
trait = values,
variance = variances,
control = self.control_locus)
else:
- qtl_result = self.dataset.genotype.regression(strains = samples,
+ self.qtl_results = self.dataset.genotype.regression(strains = samples,
trait = values,
control = self.control_locus)
else:
if self.weighted_regression:
- qtl_result = self.dataset.genotype.regression(strains = samples,
+ self.qtl_results = self.dataset.genotype.regression(strains = samples,
trait = values,
variance = variances)
else:
- qtl_result = self.dataset.genotype.regression(strains = samples,
+ self.qtl_results = self.dataset.genotype.regression(strains = samples,
trait = values)
- pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
+ #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)
+
+ #self.qtl_results = self.dataset.group.markers.markers
+ def gen_qtl_results_2(self, tempdata):
+ """Generates qtl results for plotting interval map"""
+
+ self.dataset.group.get_markers()
+ self.dataset.read_genotype_file()
+
+ 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:
@@ -131,36 +161,6 @@ class IntervalMapping(object):
self.qtl_results = self.dataset.group.markers.markers
- #def gen_qtl_results_2(self, tempdata):
- # """Generates qtl results for plotting interval map"""
- #
- # self.dataset.group.get_markers()
- # self.dataset.read_genotype_file()
- #
- # 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)
- #
- # self.qtl_results = self.dataset.group.markers.markers
-
def identify_empty_samples(self):
no_val_samples = []
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 1130fb60..9cd7d895 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -138,7 +138,7 @@ class SampleList(object):
StrainId = %s AND
CaseAttributeId = %s
group by CaseAttributeXRef.CaseAttributeId""", (
- self.this_trait.db.id, sample_id, str(attribute)))
+ self.this_trait.dataset.id, sample_id, str(attribute)))
attribute_value = result.fetchone().Value #Trait-specific attributes, if any
diff --git a/wqflask/wqflask/static/new/css/bar_chart.css b/wqflask/wqflask/static/new/css/bar_chart.css
new file mode 100644
index 00000000..ba14fe4e
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/bar_chart.css
@@ -0,0 +1,14 @@
+.axis path,
+.axis line {
+ fill: none;
+ stroke: #000;
+ shape-rendering: crispEdges;
+}
+
+.bar {
+ fill: steelblue;
+}
+
+.x.axis path {
+ display: none;
+} \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 0f16ac68..66110469 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -56,16 +56,271 @@ Stat_Table_Rows = [
url: "/glossary.html#Interquartile"
digits: 2
}
-
]
$ ->
+ class Histogram
+ constructor: (@sample_list, @sample_group) ->
+ @get_samples()
+ console.log("sample names:", @sample_names)
+
+ #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]]
+ )
+ )
+
+
+ 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)
+ )
+
+ get_attr_color_dict: () ->
+ color = d3.scale.category20()
+ @attr_color_dict = {}
+ for own key, attribute_info of js_data.attribute_names
+ this_color_dict = {}
+ for value, i in attribute_info.distinct_values
+ this_color_dict[value] = color(i)
+ @attr_color_dict[attribute_info.name] = 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_attr_color_dict()
+ console.log("samples:", @samples)
+
+ 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
+
+ sample_lists = js_data.sample_lists
+ sample_group_types = js_data.sample_group_types
+
+ new Histogram(sample_lists[0])
+
+ $('.stats_samples_group').change ->
+ $('#bar_chart').remove()
+ $('#bar_chart_container').append('<div id="bar_chart"></div>')
+ group = $(this).val()
+ console.log("group:", group)
+ if group == "samples_primary"
+ new Histogram(sample_lists[0])
+ else if group == "samples_other"
+ new Histogram(sample_lists[1])
+ else if group == "samples_all"
+ all_samples = sample_lists[0].concat sample_lists[1]
+ new Histogram(all_samples)
+
+
hide_tabs = (start) ->
for x in [start..10]
$("#stats_tabs" + x).hide()
- #hide_tabs(1)
-
# Changes stats table between all, bxd only and non-bxd, etc.
stats_mdp_change = ->
selected = $(this).val()
@@ -81,7 +336,6 @@ $ ->
current_value = parseFloat($(in_box)).toFixed(decimal_places)
- console.log("urgh:", category, value_type)
the_value = sample_sets[category][value_type]()
console.log("After running sample_sets, the_value is:", the_value)
if decimal_places > 0
@@ -121,7 +375,6 @@ $ ->
tables = ['samples_primary', 'samples_other']
for table in tables
rows = $("#" + table).find('tr')
- console.log("[fuji3] rows:", rows)
for row in rows
name = $(row).find('.edit_sample_sample_name').html()
name = $.trim(name)
@@ -180,7 +433,6 @@ $ ->
$("#stats_table").append(table)
-
process_id = (values...) ->
### Make an id or a class valid javascript by, for example, eliminating spaces ###
processed = ""
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index f554267f..4e7fe8f8 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -56,7 +56,274 @@
];
$(function() {
- 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, show_hide_outliers, stats_mdp_change, update_stat_values;
+ var Histogram, 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;
+ Histogram = (function() {
+
+ function Histogram(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);
+ 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') {
+ return _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 {
+ return _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]];
+ }
+ });
+ }
+ });
+ 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);
+ }
+ });
+ }
+
+ Histogram.prototype.get_attr_color_dict = function() {
+ var attribute_info, color, i, key, this_color_dict, value, _i, _len, _ref, _ref1, _results;
+ color = d3.scale.category20();
+ this.attr_color_dict = {};
+ _ref = js_data.attribute_names;
+ _results = [];
+ for (key in _ref) {
+ if (!__hasProp.call(_ref, key)) continue;
+ attribute_info = _ref[key];
+ this_color_dict = {};
+ _ref1 = attribute_info.distinct_values;
+ for (i = _i = 0, _len = _ref1.length; _i < _len; i = ++_i) {
+ value = _ref1[i];
+ this_color_dict[value] = color(i);
+ }
+ _results.push(this.attr_color_dict[attribute_info.name] = this_color_dict);
+ }
+ return _results;
+ };
+
+ Histogram.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);
+ }
+ }
+ this.samples = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
+ this.get_attr_color_dict();
+ return console.log("samples:", this.samples);
+ };
+
+ Histogram.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;
+ };
+
+ Histogram.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]);
+ };
+
+ Histogram.prototype.create_graph = function() {
+ this.add_x_axis(this.x_scale);
+ this.add_y_axis();
+ return this.add_bars();
+ };
+
+ Histogram.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)";
+ });
+ };
+
+ Histogram.prototype.add_y_axis = function() {
+ var yAxis;
+ yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+ return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
+ };
+
+ Histogram.prototype.add_bars = function() {
+ var _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];
+ });
+ };
+
+ Histogram.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;
+ };
+
+ return Histogram;
+
+ })();
+ sample_lists = js_data.sample_lists;
+ sample_group_types = js_data.sample_group_types;
+ new Histogram(sample_lists[0]);
+ $('.stats_samples_group').change(function() {
+ var all_samples, group;
+ $('#bar_chart').remove();
+ $('#bar_chart_container').append('<div id="bar_chart"></div>');
+ group = $(this).val();
+ console.log("group:", group);
+ if (group === "samples_primary") {
+ return new Histogram(sample_lists[0]);
+ } else if (group === "samples_other") {
+ return new Histogram(sample_lists[1]);
+ } else if (group === "samples_all") {
+ all_samples = sample_lists[0].concat(sample_lists[1]);
+ return new Histogram(all_samples);
+ }
+ });
hide_tabs = function(start) {
var x, _i, _results;
_results = [];
@@ -77,7 +344,6 @@
console.log("the_id:", id);
in_box = $(id).html;
current_value = parseFloat($(in_box)).toFixed(decimal_places);
- console.log("urgh:", category, value_type);
the_value = sample_sets[category][value_type]();
console.log("After running sample_sets, the_value is:", the_value);
if (decimal_places > 0) {
@@ -127,7 +393,6 @@
for (_i = 0, _len = tables.length; _i < _len; _i++) {
table = tables[_i];
rows = $("#" + table).find('tr');
- console.log("[fuji3] rows:", rows);
for (_j = 0, _len1 = rows.length; _j < _len1; _j++) {
row = rows[_j];
name = $(row).find('.edit_sample_sample_name').html();
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 7e149506..d675b801 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -9,55 +9,76 @@
{{ header("Correlation", 'Trait: {} Dataset: {}'.format(this_trait.name, dataset.name)) }}
- <table id="corr_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <th>Trait</th>
- <th>Symbol</th>
- <th>Alias</th>
- <th>Description</th>
- <th>Location</th>
- <th>Mean Expr</th>
- <th>Max LRS</th>
- <th>Max LRS Location</th>
- {% if corr_method == 'pearson' %}
- <th>Sample r</th>
- <th>N Cases</th>
- <th>Sample p(r)</th>
- <th>Lit Corr</th>
- <th>Tissue r</th>
- <th>Tissue p(r)</th>
- {% else %}
- <th>Sample rho</th>
- <th>Sample p(rho)</th>
- <th>Lit Corr</th>
- <th>Tissue rho</th>
- <th>Tissue p(rho)</th>
- {% endif %}
+ <div class="container">
+ <div class="page-header">
+ <h1>Correlation Table</h1>
+ </div>
+
+ <p>Values of record {{ this_trait.name }} in the <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a>
+ dataset were compared to all records in the <a href="/dbdoc/{{target_dataset.fullname}}">{{ target_dataset.fullname }}</a>
+ dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed.
+ You can resort this list by clicking the headers. Select the Record ID to open the trait data
+ and analysis page.
+ </p>
+
+ <div>
+ <table id="corr_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <th>Trait</th>
+ <th>Symbol</th>
+ <th>Description</th>
+ <th>Location</th>
+ <th>Mean Expr</th>
+ <th>Max LRS</th>
+ <th>Max LRS Location</th>
+ {% if corr_method == 'pearson' %}
+ <th>Sample r</th>
+ <th>N Cases</th>
+ <th>Sample p(r)</th>
+ <th>Lit Corr</th>
+ <th>Tissue r</th>
+ <th>Tissue p(r)</th>
+ {% else %}
+ <th>Sample rho</th>
+ <th>N Cases</th>
+ <th>Sample p(rho)</th>
+ <th>Lit Corr</th>
+ <th>Tissue rho</th>
+ <th>Tissue p(rho)</th>
+ {% endif %}
+ </tr>
+ </thead>
+ <tbody>
+ {% for trait in correlation_results %}
+ <tr>
+ <td><a href="/show_trait?trait_id={{trait.name}}&amp;dataset={{trait.dataset.name}}">{{ trait.name }}</a></td>
+ <td>{{ trait.symbol }}</td>
+ <td>{{ trait.description }} <br><br> <b>Aliases</b>: {{ trait.alias }}</td>
+ <td>Chr{{ trait.chr }}: {{'%0.3f'|format(trait.mb) }}</td>
+ <td>{{'%0.3f'|format(trait.mean)}}</td>
+ <td>{{'%0.3f'|format(trait.lrs)}}</td>
+ <td>Chr{{ trait.locus_chr }}: {{'%0.3f'|format(trait.locus_mb) }}</td>
+ <td>{{'%0.3f'|format(trait.sample_r)}}</td>
+ <td>{{ trait.num_overlap }}</td>
+ <td>{{'%0.3e'|format(trait.sample_p)}}</td>
+ <td>{{'%0.3f'|format(trait.lit_corr)}}</td>
+ <td>{{'%0.3f'|format(trait.tissue_corr)}}</td>
+ <td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
- </tr>
- </thead>
- <tbody>
- {% for trait in correlation_results %}
- <tr>
- <td><a href="/show_trait?trait_id={{trait.name}}&amp;dataset={{trait.dataset.name}}">{{ trait.name }}</a></td>
- <td>{{ trait.symbol }}</td>
- <td>{{ trait.alias }}</td>
- <td>{{ trait.description }}</td>
- <td>Chr{{ trait.chr }}:{{trait.mb}}</td>
- <td>{{'%0.3f'|format(trait.mean)}}</td>
- <td>{{'%0.3f'|format(trait.lrs)}}</td>
- <td>Chr{{ trait.locus_chr }}:{{'%0.6f'|format(trait.locus_mb)}}</td>
- <td>{{'%0.3f'|format(trait.sample_r)}}</td>
- <td>{{ trait.num_overlap }}</td>
- <td>{{'%0.3e'|format(trait.sample_p)}}</td>
- <td>{{'%0.3f'|format(trait.lit_corr)}}</td>
- <td>{{'%0.3f'|format(trait.tissue_corr)}}</td>
- <td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
+ <br />
+
+<!-- <button class="btn"><i class="icon-ok"></i> Select</button>
+ <button class="btn"><i class="icon-remove"></i> Deselect</button>
+ <button class="btn"><i class="icon-resize-vertical"></i> Invert</button>
+ <button class="btn"><i class="icon-plus-sign"></i> Add</button>
+ <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>-->
+ </div>
+ </div>
{% endblock %}
{% block js %}
@@ -92,4 +113,4 @@
console.timeEnd("Creating table");
});
</script>
-{% endblock %} \ No newline at end of file
+{% endblock %}
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index 2f268c5a..fe6f3f65 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -3,15 +3,14 @@
{% block content %}
<!-- Start of body -->
- {{ header("QuickSearch Results",
- 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
+ {{ header("QuickSearch Results") }}
<div class="container">
<div class="page-header">
<h1>Your Search</h1>
</div>
- <p>We across all data sets to find all records that match:</p>
+ <p>We searched across all data sets to find all records that match:</p>
<ul>
{% if search_terms %}
@@ -276,7 +275,7 @@
console.time("Creating table");
$('#pheno_results, #mrna_assay_results, #geno_results').dataTable( {
//"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
- "sDom": "lTftipr",
+ //"sDom": "lTftipr",
"oTableTools": {
"aButtons": [
"copy",
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index b29e6482..5bd6534c 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -10,7 +10,7 @@
<h1>Your Search</h1>
</div>
- <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a><//>
+ <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a></p>
<p>To find all records that match:</p>
<ul>
@@ -85,7 +85,6 @@
<button class="btn" id="add"><i class="icon-plus-sign"></i> Add</button>
<button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
</div>
-
</div>
<div id="myModal"></div>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index e3c84de7..5d77750c 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/bar_chart.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" />
{% endblock %}
@@ -28,7 +29,7 @@
</div>
{% include 'show_trait_details.html' %}
- {# {% include 'show_trait_statistics.html' %} #}
+ {% include 'show_trait_statistics_new.html' %}
{% include 'show_trait_calculate_correlations.html' %}
{% include 'show_trait_mapping_tools.html' %}
{% include 'show_trait_edit_data.html' %}
diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html
new file mode 100644
index 00000000..105c4f95
--- /dev/null
+++ b/wqflask/wqflask/templates/show_trait_statistics_new.html
@@ -0,0 +1,29 @@
+<div>
+ <br>
+ <h2>Charts and Figures</h2>
+ <div class="well form-horizontal">
+ {% if sample_groups|length > 1 %}
+ <select class="stats_samples_group">
+ {% for group, pretty_group in sample_group_types.items() %}
+ <option value="{{ group }}">{{ pretty_group }}</option>
+ {% endfor %}
+ </select>
+ {% endif %}
+ {% if sample_groups[0].attributes %}
+ <div class="input-append">
+ <select id="color_attribute" size=1>
+ <option value="None">None</option>
+ {% for attribute in sample_groups[0].attributes %}
+ <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
+ {{ sample_groups[0].attributes[attribute].name }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ {% endif %}
+ <button type="button" id="update_bar_chart">Sort By Value</button>
+ <div id="bar_chart_container">
+ <div id="bar_chart"></div>
+ </div>
+
+ </div>
+</div> \ No newline at end of file
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 6c9addbc..22973045 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -32,6 +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.correlation import show_corr_results
from utility import temp_data
@@ -247,6 +248,49 @@ def marker_regression_page():
return rendered_template
+@app.route("/interval_mapping", methods=('POST',))
+def interval_mapping_page():
+ initial_start_vars = request.form
+ temp_uuid = initial_start_vars['temp_uuid']
+ wanted = (
+ 'trait_id',
+ 'dataset',
+ 'suggestive'
+ )
+
+ start_vars = {}
+ for key, value in initial_start_vars.iteritems():
+ if key in wanted or key.startswith(('value:')):
+ start_vars[key] = value
+
+ version = "v1"
+ key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
+ print("key is:", pf(key))
+ with Bench("Loading cache"):
+ result = Redis.get(key)
+
+ if result:
+ print("Cache hit!!!")
+ with Bench("Loading results"):
+ result = pickle.loads(result)
+ else:
+ print("Cache miss!!!")
+ template_vars = interval_mapping.IntervalMapping(start_vars, temp_uuid)
+
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
+
+ result = template_vars.__dict__
+
+ #causeerror
+ Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
+ Redis.expire(key, 60*60)
+
+ with Bench("Rendering template"):
+ rendered_template = render_template("interval_mapping.html", **result)
+
+ return rendered_template
@app.route("/corr_compute", methods=('POST',))
def corr_compute_page():
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-21 11:51:09 +0000