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-rw-r--r--wqflask/base/webqtlCaseData.py11
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py86
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py41
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css7
-rw-r--r--wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js222
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js372
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js545
-rw-r--r--wqflask/wqflask/templates/show_trait.html289
-rw-r--r--wqflask/wqflask/templates/show_trait_transform_and_filter.html42
9 files changed, 789 insertions, 826 deletions
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 2844cedd..3cf2d80d 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -41,6 +41,8 @@ class webqtlCaseData:
self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word)
self.outlier = None # Not set to True/False until later
+ self.first_attr_col = self.get_first_attr_col()
+
def __repr__(self):
case_data_string = "<webqtlCaseData> "
if self.value is not None:
@@ -79,3 +81,12 @@ class webqtlCaseData:
if self.num_cases is not None:
return "%s" % self.num_cases
return "x"
+
+ def get_first_attr_col(self):
+ col_num = 4
+ if self.variance is not None:
+ col_num += 2
+ if self.num_cases is not None:
+ col_num += 1
+
+ return col_num \ No newline at end of file
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index ad78ebcc..356db7bc 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -1,21 +1,20 @@
from __future__ import absolute_import, print_function, division
-from flask import Flask, g
-
-from base import webqtlCaseData
-from utility import webqtlUtil, Plot, Bunch
-from base.trait import GeneralTrait
+import itertools
import numpy as np
-from scipy import stats
+from flask import Flask, g
from pprint import pformat as pf
+from scipy import stats
-import simplejson as json
-
-import itertools
+from base import webqtlCaseData
+from base.trait import GeneralTrait
+from utility import logger
+from utility import webqtlUtil
+from utility import Plot
+from utility import Bunch
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = logger.getLogger(__name__ )
class SampleList(object):
def __init__(self,
@@ -35,25 +34,22 @@ class SampleList(object):
self.get_attributes()
- #self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
-
if self.this_trait and self.dataset:
self.get_extra_attribute_values()
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
- if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait
+ if type(self.this_trait) is list: # ZS: self.this_trait will be a list if it is a Temp trait
if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X':
sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
else:
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
else:
- #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
+ # ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
try:
sample = self.this_trait.data[sample_name]
except KeyError:
- #logger.debug("No sample %s, let's create it now" % sample_name)
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
sample.extra_info = {}
@@ -63,15 +59,13 @@ class SampleList(object):
sample.this_id = str(counter)
- #### For extra attribute columns; currently only used by several datasets - Zach
+ # ZS: For extra attribute columns; currently only used by several datasets
if self.sample_attribute_values:
sample.extra_attributes = self.sample_attribute_values.get(sample_name, {})
- #logger.debug("sample.extra_attributes is", pf(sample.extra_attributes))
self.sample_list.append(sample)
- #logger.debug("attribute vals are", pf(self.sample_attribute_values))
-
+ self.se_exists = any(sample.variance for sample in self.sample_list)
self.do_outliers()
def __repr__(self):
@@ -104,7 +98,6 @@ class SampleList(object):
self.attributes = {}
for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
key, name = attr
- #logger.debug("radish: %s - %s" % (key, name))
self.attributes[key] = Bunch()
self.attributes[key].name = name
self.attributes[key].distinct_values = [item.Value for item in values]
@@ -141,8 +134,8 @@ class SampleList(object):
for item in items:
attribute_value = item.Value
- #ZS: If it's an int, turn it into one for sorting
- #(for example, 101 would be lower than 80 if they're strings instead of ints)
+ # ZS: If it's an int, turn it into one for sorting
+ # (for example, 101 would be lower than 80 if they're strings instead of ints)
try:
attribute_value = int(attribute_value)
except ValueError:
@@ -151,53 +144,6 @@ class SampleList(object):
attribute_values[self.attributes[item.Id].name] = attribute_value
self.sample_attribute_values[sample_name] = attribute_values
- def se_exists(self):
- """Returns true if SE values exist for any samples, otherwise false"""
-
- return any(sample.variance for sample in self.sample_list)
-
-# def get_transform_vals(dataset, trait):
-# es = get_elasticsearch_connection(for_user=False)
-
-# logger.info("DATASET NAME:", dataset.name)
-
-# query = '{"bool": {"must": [{"match": {"name": "%s"}}, {"match": {"dataset": "%s"}}]}}' % (trait.name, dataset.name)
-
-# es_body = {
-# "query": {
-# "bool": {
-# "must": [
-# {
-# "match": {
-# "name": "%s" % (trait.name)
-# }
-# },
-# {
-# "match": {
-# "dataset": "%s" % (dataset.name)
-# }
-# }
-# ]
-# }
-# }
-# }
-
-# response = es.search( index = "traits", doc_type = "trait", body = es_body )
-# logger.info("THE RESPONSE:", response)
-# results = response['hits']['hits']
-
-# if len(results) > 0:
-# samples = results[0]['_source']['samples']
-
-# sample_dict = {}
-# for sample in samples:
-# sample_dict[sample['name']] = sample['qnorm']
-
-# #logger.info("SAMPLE DICT:", sample_dict)
-# return sample_dict
-# else:
-# return None
-
def natural_sort_key(x):
"""Get expected results when using as a key for sort - ints or strings are sorted properly"""
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f188fd9d..30b03e66 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -43,8 +43,6 @@ logger = getLogger(__name__ )
class ShowTrait(object):
def __init__(self, kw):
- logger.debug("in ShowTrait, kw are:", kw)
-
if 'trait_id' in kw and kw['dataset'] != "Temp":
self.temp_trait = False
self.trait_id = kw['trait_id']
@@ -152,6 +150,7 @@ class ShowTrait(object):
#self.nearest_marker1 = ""
#self.nearest_marker2 = ""
+
self.make_sample_lists()
self.qnorm_vals = quantile_normalize_vals(self.sample_groups)
@@ -275,7 +274,9 @@ class ShowTrait(object):
data_scale = self.dataset.data_scale,
sample_group_types = self.sample_group_types,
sample_lists = sample_lists,
- attribute_names = self.sample_groups[0].attributes,
+ se_exists = self.sample_groups[0].se_exists,
+ has_num_cases = self.has_num_cases,
+ attributes = self.sample_groups[0].attributes,
categorical_vars = ",".join(categorical_var_list),
num_values = self.num_values,
qnorm_values = self.qnorm_vals,
@@ -395,6 +396,7 @@ class ShowTrait(object):
return_results_menu_selected = return_results_menu_selected,)
def make_sample_lists(self):
+
all_samples_ordered = self.dataset.group.all_samples_ordered()
parent_f1_samples = []
@@ -403,13 +405,18 @@ class ShowTrait(object):
primary_sample_names = list(all_samples_ordered)
+
if not self.temp_trait:
other_sample_names = []
- for sample in self.this_trait.data.keys():
- if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names):
- primary_sample_names.append(self.this_trait.data[sample].name)
- primary_sample_names.remove(self.this_trait.data[sample].name2)
- elif sample not in all_samples_ordered:
+
+ for sample in self.this_trait.data:
+ if self.this_trait.data[sample].name2 != self.this_trait.data[sample].name:
+ if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names):
+ primary_sample_names.append(self.this_trait.data[sample].name)
+ primary_sample_names.remove(self.this_trait.data[sample].name2)
+
+ all_samples_set = set(all_samples_ordered)
+ if sample not in all_samples_set:
all_samples_ordered.append(sample)
other_sample_names.append(sample)
@@ -422,6 +429,7 @@ class ShowTrait(object):
primary_header = "%s Only" % (self.dataset.group.name)
else:
primary_header = "Samples"
+
primary_samples = SampleList(dataset = self.dataset,
sample_names=primary_sample_names,
this_trait=self.this_trait,
@@ -454,6 +462,7 @@ class ShowTrait(object):
self.primary_sample_names = primary_sample_names
self.dataset.group.allsamples = all_samples_ordered
+
def quantile_normalize_vals(sample_groups):
def normf(trait_vals):
ranked_vals = ss.rankdata(trait_vals)
@@ -492,6 +501,7 @@ def quantile_normalize_vals(sample_groups):
return qnorm_by_group
+
def get_z_scores(sample_groups):
zscore_by_group = []
for sample_type in sample_groups:
@@ -516,11 +526,10 @@ def get_z_scores(sample_groups):
return zscore_by_group
+
def get_nearest_marker(this_trait, this_db):
this_chr = this_trait.locus_chr
- logger.debug("this_chr:", this_chr)
this_mb = this_trait.locus_mb
- logger.debug("this_mb:", this_mb)
#One option is to take flanking markers, another is to take the two (or one) closest
query = """SELECT Geno.Name
FROM Geno, GenoXRef, GenoFreeze
@@ -531,7 +540,6 @@ def get_nearest_marker(this_trait, this_db):
ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb)
logger.sql(query)
result = g.db.execute(query).fetchall()
- logger.debug("result:", result)
if result == []:
return ""
@@ -539,13 +547,14 @@ def get_nearest_marker(this_trait, this_db):
else:
return result[0][0]
+
def get_table_widths(sample_groups, has_num_cases=False):
stats_table_width = 250
if len(sample_groups) > 1:
stats_table_width = 450
trait_table_width = 380
- if sample_groups[0].se_exists():
+ if sample_groups[0].se_exists:
trait_table_width += 80
if has_num_cases:
trait_table_width += 80
@@ -555,6 +564,7 @@ def get_table_widths(sample_groups, has_num_cases=False):
return stats_table_width, trait_table_width
+
def has_num_cases(this_trait):
has_n = False
if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno":
@@ -565,6 +575,7 @@ def has_num_cases(this_trait):
return has_n
+
def get_trait_units(this_trait):
unit_type = ""
inside_brackets = False
@@ -584,6 +595,7 @@ def get_trait_units(this_trait):
return unit_type
+
def check_if_attr_exists(the_trait, id_type):
if hasattr(the_trait, id_type):
if getattr(the_trait, id_type) == None or getattr(the_trait, id_type) == "":
@@ -593,6 +605,7 @@ def check_if_attr_exists(the_trait, id_type):
else:
return False
+
def get_ncbi_summary(this_trait):
if check_if_attr_exists(this_trait, 'geneid'):
#ZS: Need to switch this try/except to something that checks the output later
@@ -605,6 +618,7 @@ def get_ncbi_summary(this_trait):
else:
return None
+
def get_categorical_variables(this_trait, sample_list):
categorical_var_list = []
@@ -623,6 +637,7 @@ def get_categorical_variables(this_trait, sample_list):
return categorical_var_list
+
def get_genotype_scales(genofiles):
geno_scales = {}
if type(genofiles) is list:
@@ -634,6 +649,7 @@ def get_genotype_scales(genofiles):
return geno_scales
+
def get_scales_from_genofile(file_location):
geno_path = locate_ignore_error(file_location, 'genotype')
@@ -686,6 +702,7 @@ def get_scales_from_genofile(file_location):
if i > first_marker_line + 10:
break
+
#ZS: This assumes that both won't be all zero, since if that's the case mapping shouldn't be an option to begin with
if mb_all_zero:
return [["morgan", "cM"]]
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index a04b2243..42009a70 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -53,6 +53,13 @@ table.dataTable.cell-border tbody tr td:first-child {
border-left: 1px solid #ccc;
}
+.checkbox {
+ min-height: 20px;
+}
+
+.trait_value_input {
+ text-align: right;
+
.glyphicon {
position: relative;
top: 2px;
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
new file mode 100644
index 00000000..97b71306
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -0,0 +1,222 @@
+// ZS: This file initializes the tables for the show_trait page
+
+// ZS: This variable is just created to get the column position of the first case attribute (if case attributes exist), since it's needed to set the row classes in createdRow for the DataTable
+var attribute_start_pos = 3;
+if (js_data.se_exists) {
+ attribute_start_pos += 2;
+}
+if (js_data.has_num_cases === true) {
+ attribute_start_post += 1;
+}
+
+build_columns = function() {
+ let column_list = [
+ {
+ 'data': null,
+ 'orderDataType': "dom-checkbox",
+ 'searchable' : false,
+ 'render': function(data, type, row, meta) {
+ return '<input type="checkbox" name="searchResult" class="checkbox edit_sample_checkbox" value="">'
+ }
+ },
+ {
+ 'title': "ID",
+ 'type': "natural",
+ 'searchable' : false,
+ 'data': "this_id"
+ },
+ {
+ 'title': "Sample",
+ 'type': "natural",
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ return '<span class="edit_sample_sample_name">' + data.name + '</span>'
+ }
+ },
+ {
+ 'title': "<div style='text-align: right;'>Value</div>",
+ 'orderDataType': "dom-input",
+ 'type': "cust-txt",
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ if (data.value == null) {
+ return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
+ } else {
+ return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
+ }
+ }
+ }
+ ];
+
+ if (js_data.se_exists) {
+ column_list.push(
+ {
+ 'bSortable': false,
+ 'type': "natural",
+ 'data': null,
+ 'searchable' : false,
+ 'render': function(data, type, row, meta) {
+ return '±'
+ }
+ },
+ {
+ 'title': "<div style='text-align: right;'>SE</div>",
+ 'orderDataType': "dom-input",
+ 'type': "cust-txt",
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ if (data.variance == null) {
+ return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
+ } else {
+ return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
+ }
+ }
+ }
+ );
+ }
+
+ if (js_data.has_num_cases === "true") {
+ column_list.push(
+ {
+ 'title': "<div style='text-align: right;'>N</div>",
+ 'orderDataType': "dom-input",
+ 'type': "cust-txt",
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ if (data.num_cases == null || data.num_cases == undefined) {
+ return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
+ } else {
+ return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
+ }
+ }
+ }
+ );
+ }
+
+ attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name > js_data.attributes[b].name) ? 1 : -1)
+ for (i = 0; i < attr_keys.length; i++){
+ column_list.push(
+ {
+ 'title': "<div style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>",
+ 'type': "natural",
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ attr_name = Object.keys(data.extra_attributes).sort((a, b) => (a > b) ? 1 : -1)[meta.col - data.first_attr_col]
+ if (attr_name != null && attr_name != undefined){
+ return data.extra_attributes[attr_name]
+ } else {
+ return ""
+ }
+ }
+ }
+ )
+ }
+
+ return column_list
+}
+
+var primary_table = $('#samples_primary').DataTable( {
+ 'initComplete': function(settings, json) {
+ $('.edit_sample_value').change(function() {
+ edit_data_change();
+ });
+ },
+ 'createdRow': function ( row, data, index ) {
+ $(row).attr('id', "Primary_" + data.this_id)
+ $(row).addClass("value_se");
+ if (data.outlier) {
+ $(row).addClass("outlier");
+ }
+ $('td', row).eq(1).addClass("column_name-Index")
+ $('td', row).eq(2).addClass("column_name-Sample")
+ $('td', row).eq(3).addClass("column_name-Value")
+ if (js_data.se_exists) {
+ $('td', row).eq(5).addClass("column_name-SE")
+ if (js_data.has_num_cases === "true") {
+ $('td', row).eq(6).addClass("column_name-num_cases")
+ } else {
+ if (js_data.has_num_cases === "true") {
+ $('td', row).eq(4).addClass("column_name-num_cases")
+ }
+ }
+ } else {
+ if (js_data.has_num_cases === "true") {
+ $('td', row).eq(4).addClass("column_name-num_cases")
+ }
+ }
+
+ sorted_key_list = Object.keys(js_data.attributes).sort()
+ for (i=0; i < sorted_key_list.length; i++) {
+ $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
+ $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
+ }
+ },
+ 'data': js_data['sample_lists'][0],
+ 'columns': build_columns(),
+ 'order': [[1, "asc"]],
+ 'sDom': "Ztr",
+ 'autoWidth': true,
+ 'orderClasses': true,
+ "scrollY": "50vh",
+ 'scroller': true,
+ 'scrollCollapse': true
+} );
+
+primary_table.on( 'order.dt search.dt draw.dt', function () {
+ primary_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) {
+ cell.innerHTML = i+1;
+ } );
+} ).draw();
+
+$('#primary_searchbox').on( 'keyup', function () {
+ primary_table.search($(this).val()).draw();
+} );
+
+if (js_data.sample_lists.length > 1){
+ var other_table = $('#samples_other').DataTable( {
+ 'initComplete': function(settings, json) {
+ $('.edit_sample_value').change(function() {
+ edit_data_change();
+ });
+ },
+ 'createdRow': function ( row, data, index ) {
+ $(row).attr('id', "Primary_" + data.this_id)
+ $(row).addClass("value_se");
+ if (data.outlier) {
+ $(row).addClass("outlier");
+ }
+ $('td', row).eq(1).addClass("column_name-Index")
+ $('td', row).eq(2).addClass("column_name-Sample")
+ $('td', row).eq(3).addClass("column_name-Value")
+ if (js_data.se_exists) {
+ $('td', row).eq(5).addClass("column_name-SE")
+ if (js_data.has_num_cases === "true") {
+ $('td', row).eq(6).addClass("column_name-num_cases")
+ } else {
+ if (js_data.has_num_cases === "true") {
+ $('td', row).eq(4).addClass("column_name-num_cases")
+ }
+ }
+ } else {
+ if (js_data.has_num_cases === "true") {
+ $('td', row).eq(4).addClass("column_name-num_cases")
+ }
+ }
+
+ sorted_key_list = Object.keys(js_data.attributes).sort()
+ for (i=0; i < sorted_key_list.length; i++) {
+ $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
+ $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
+ }
+ },
+ 'data': js_data['sample_lists'][1],
+ 'columns': build_columns(),
+ 'order': [[1, "asc"]],
+ 'sDom': "Ztr",
+ 'autoWidth': true,
+ 'orderClasses': true,
+ "scrollY": "50vh",
+ 'scroller': true,
+ 'scrollCollapse': true
+ } );
+} \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index c0ab639e..397adb52 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -440,38 +440,47 @@ edit_data_change = function() {
samples_other: {},
samples_all: {}
};
+
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();
- checkbox = $(row).find(".edit-sample-checkbox");
- if (is_number(real_value) && real_value !== "") {
- real_value = parseFloat(real_value);
- sample_sets[table].add_value(real_value);
- real_variance = $(row).find('.edit-sample-se').val();
- if (is_number(real_variance)) {
- real_variance = parseFloat(real_variance);
- } else {
- real_variance = null;
- }
- real_dict = {
- value: real_value,
- variance: real_variance
- };
- root.selected_samples[table][name] = real_dict;
- if (!(name in already_seen)) {
- sample_sets['samples_all'].add_value(real_value);
- root.selected_samples['samples_all'][name] = real_dict;
- already_seen[name] = true;
+ if ($('#' + table).length){
+ table_api = $('#' + table).DataTable();
+ sample_vals = [];
+ name_nodes = table_api.column(2).nodes().to$();
+ val_nodes = table_api.column(3).nodes().to$();
+ var_nodes = table_api.column(5).nodes().to$();
+ for (_j = 0; _j < val_nodes.length; _j++){
+ sample_val = val_nodes[_j].childNodes[0].value
+ sample_name = $.trim(name_nodes[_j].childNodes[0].textContent)
+ if (is_number(sample_val) && sample_val !== "") {
+ sample_val = parseFloat(sample_val);
+ sample_sets[table].add_value(sample_val);
+ if (typeof var_nodes !== 'undefined'){
+ sample_var = null;
+ } else {
+ sample_var = var_nodes[_j].childNodes[0].value
+ if (is_number(sample_var)) {
+ sample_var = parseFloat(sample_var)
+ } else {
+ sample_var = null;
+ }
+ }
+ sample_dict = {
+ value: sample_val,
+ variance: sample_var
+ }
+ root.selected_samples[table][sample_name] = sample_dict;
+ if (!(sample_name in already_seen)) {
+ sample_sets['samples_all'].add_value(sample_val);
+ root.selected_samples['samples_all'][sample_name] = sample_dict;
+ already_seen[sample_name] = true;
+ }
}
}
}
}
+
update_stat_values(sample_sets);
if ($('#histogram').hasClass('js-plotly-plot')){
@@ -490,6 +499,7 @@ edit_data_change = function() {
return update_prob_plot();
}
};
+
show_hide_outliers = function() {
var label;
label = $('#show_hide_outliers').val();
@@ -500,6 +510,7 @@ show_hide_outliers = function() {
return console.log("Should be now Hide Outliers");
}
};
+
on_corr_method_change = function() {
var corr_method;
corr_method = $('select[name=corr_type]').val();
@@ -514,10 +525,30 @@ on_corr_method_change = function() {
$('select[name=corr_type]').change(on_corr_method_change);
submit_special = function(url) {
+ get_table_contents_for_form_submit("trait_data_form");
$("#trait_data_form").attr("action", url);
$("#trait_data_form").submit();
};
+get_table_contents_for_form_submit = function(form_id) {
+ // Borrowed code from - https://stackoverflow.com/questions/31418047/how-to-post-data-for-the-whole-table-using-jquery-datatables
+ let this_form = $("#" + form_id);
+ var params = primary_table.$('input').serializeArray();
+
+ $.each(params, function(){
+ // If element doesn't exist in DOM
+ if(!$.contains(document, this_form[this.name])){
+ // Create a hidden element
+ this_form.append(
+ $('<input>')
+ .attr('type', 'hidden')
+ .attr('name', this.name)
+ .val(this.value)
+ );
+ }
+ });
+}
+
var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
@@ -538,10 +569,9 @@ populate_sample_attributes_values_dropdown = function() {
var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results;
$('#attribute_values').empty();
sample_attributes = {};
- _ref = js_data.attribute_names;
- for (key in _ref) {
- if (!__hasProp.call(_ref, key)) continue;
- attribute_info = _ref[key];
+ attr_keys = Object.keys(js_data.attributes).sort();
+ for (i=0; i < attr_keys.length; i++) {
+ attribute_info = js_data.attributes[attr_keys[i]];
sample_attributes[attribute_info.name] = attribute_info.distinct_values;
}
selected_attribute = $('#exclude_menu').val().replace("_", " ");
@@ -549,13 +579,17 @@ populate_sample_attributes_values_dropdown = function() {
_results = [];
for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
value = _ref1[_i];
- _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
+ if (value != ""){
+ _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
+ }
}
return _results;
};
-if (Object.keys(js_data.attribute_names).length > 0) {
+
+if (Object.keys(js_data.attributes).length){
populate_sample_attributes_values_dropdown();
}
+
$('#exclude_menu').change(populate_sample_attributes_values_dropdown);
block_by_attribute_value = function() {
var attribute_name, cell_class, exclude_by_value;
@@ -580,20 +614,6 @@ block_by_index = function() {
_ref = index_string.split(",");
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
index_set = _ref[_i];
- /*
- if (index_set.indexOf('<') !== -1) {
- try {
- start_index = parseInt(index_set.split("<")[0]);
- end_index = parseInt(index_set.split("<")[1]);
- for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) {
- index_list.push(index);
- }
- } catch (_error) {
- error = _error;
- alert("Syntax error");
- }
- }
- */
if (index_set.indexOf('-') !== -1) {
try {
start_index = parseInt(index_set.split("-")[0]);
@@ -611,19 +631,19 @@ block_by_index = function() {
}
}
_results = [];
+ let block_group = $('#block_group').val();
+ if (block_group === "other") {
+ table_api = $('#samples_other').DataTable();
+ } else {
+ table_api = $('#samples_primary').DataTable();
+ }
+ val_nodes = table_api.column(3).nodes().to$();
for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
index = index_list[_k];
- if ($('#block_group').val() === "primary") {
- _results.push($('#samples_primary').find('td.column_name-Index').filter(function() { return $(this).text() == index.toString() }).closest('tr').find('.trait-value-input').val("x"));
- } else if ($('#block_group').val() === "other") {
- _results.push($('#samples_other').find('td.column_name-Index').filter(function() { return $(this).text() == index.toString() }).closest('tr').find('.trait-value-input').val("x"));
- } else {
- _results.push(void 0);
- }
+ val_nodes[index - 1].childNodes[0].value = "x";
+
}
- return _results;
};
-$('#block_by_index').click(block_by_index);
hide_no_value = function() {
return $('.value_se').each((function(_this) {
@@ -635,6 +655,7 @@ hide_no_value = function() {
})(this));
};
$('#hide_no_value').click(hide_no_value);
+
block_outliers = function() {
return $('.outlier').each((function(_this) {
return function(_index, element) {
@@ -643,177 +664,194 @@ block_outliers = function() {
})(this));
};
$('#block_outliers').click(block_outliers);
+
reset_samples_table = function() {
$('input[name="transform"]').val("");
$('span[name="transform_text"]').text("")
- return $('.trait-value-input').each((function(_this) {
- return function(_index, element) {
- $(element).val($(element).data('value'));
- return $(element).parents('.value_se').show();
- };
- })(this));
+ tables = ['samples_primary', 'samples_other'];
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ if ($('#' + table).length) {
+ table_api = $('#' + table).DataTable();
+ val_nodes = table_api.column(3).nodes().to$();
+ for (i = 0; i < val_nodes.length; i++) {
+ this_node = val_nodes[i].childNodes[0];
+ this_node.value = this_node.attributes["data-value"].value;
+ }
+ if (js_data.se_exists){
+ se_nodes = table_api.column(5).nodes().to$();
+ for (i = 0; i < val_nodes.length; i++) {
+ this_node = val_nodes[i].childNodes[0];
+ this_node.value = this_node.attributes["data-value"].value;
+ }
+ }
+ }
+ }
};
$('.reset').click(function() {
reset_samples_table();
edit_data_change();
});
-log2_normalize_data = function(zero_to_one_vals_exist) {
- return $('.trait-value-input').each((function(_this) {
- return function(_index, element) {
- current_value = $(element).data("value")
- if(isNaN(current_value)) {
- return current_value
- } else {
- if (zero_to_one_vals_exist){
- current_value = parseFloat(current_value) + 1;
+check_for_zero_to_one_vals = function() {
+ tables = ['samples_primary', 'samples_other'];
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ if ($('#' + table).length) {
+ table_api = $('#' + table).DataTable();
+ val_nodes = table_api.column(3).nodes().to$();
+ for (i = 0; i < val_nodes.length; i++) {
+ this_node = val_nodes[i].childNodes[0];
+ if(!isNaN(this_node.value)) {
+ if (0 <= this_node.value && this_node.value < 1){
+ return true
+ }
}
- $(element).val(Math.log2(current_value).toFixed(3));
- return Math.log2(current_value).toFixed(3)
}
- };
- })(this));
-};
+ }
+ }
+ return false
+}
-log10_normalize_data = function(zero_to_one_vals_exist) {
- return $('.trait-value-input').each((function(_this) {
- return function(_index, element) {
- current_value = $(element).data("value")
- if(isNaN(current_value)) {
- return current_value
- } else {
- if (zero_to_one_vals_exist){
- current_value = parseFloat(current_value) + 1;
- }
- $(element).val(Math.log10(current_value).toFixed(3));
- return Math.log10(current_value).toFixed(3)
- }
- };
- })(this));
+log2_data = function(this_node) {
+ current_value = this_node.value;
+ original_value = this_node.attributes['data-value'].value;
+ if(!isNaN(current_value) && !isNaN(original_value)) {
+ if (zero_to_one_vals_exist){
+ original_value = parseFloat(original_value) + 1;
+ }
+ this_node.value = Math.log2(original_value).toFixed(3);
+ }
};
+log10_data = function() {
+ current_value = this_node.value;
+ original_value = this_node.attributes['data-value'].value;
+ if(!isNaN(current_value) && !isNaN(original_value)) {
+ if (zero_to_one_vals_exist){
+ original_value = parseFloat(original_value) + 1;
+ }
+ this_node.value = Math.log10(original_value).toFixed(3);
+ }
+};
-sqrt_normalize_data = function() {
- return $('.edit-sample-value').each((function(_this) {
- return function(_index, element) {
- current_value = parseFloat($(element).data("value")) + 1;
- if(isNaN(current_value)) {
- return current_value
- } else {
- $(element).val(Math.sqrt(current_value).toFixed(3));
- return Math.sqrt(current_value).toFixed(3)
- }
- };
- })(this));
+sqrt_data = function() {
+ current_value = this_node.value;
+ original_value = this_node.attributes['data-value'].value;
+ if(!isNaN(current_value) && !isNaN(original_value)) {
+ if (zero_to_one_vals_exist){
+ original_value = parseFloat(original_value) + 1;
+ }
+ this_node.value = Math.sqrt(original_value).toFixed(3);
+ }
};
invert_data = function() {
- return $('.edit-sample-value').each((function(_this) {
- return function(_index, element) {
- current_value = parseFloat($(element).val());
- if(isNaN(current_value)) {
- return current_value
- } else {
- $(element).val(-(current_value));
- return -(current_value)
- }
- };
- })(this));
+ current_value = this_node.value;
+ if(!isNaN(current_value)) {
+ this_node.value = parseFloat(-(current_value)).toFixed(3);
+ }
};
-
qnorm_data = function() {
- return $('.edit-sample-value').each((function(_this) {
- return function(_index, element) {
- current_value = parseFloat($(element).data("value")) + 1;
- if(isNaN(current_value)) {
- return current_value
- } else {
- $(element).val($(element).data("qnorm"));
- return $(element).data("qnorm");
- }
- };
- })(this));
+ current_value = this_node.value;
+ qnorm_value = this_node.attributes['data-qnorm'].value;
+ if(!isNaN(current_value)) {
+ this_node.value = qnorm_value;
+ }
};
zscore_data = function() {
- return $('.edit-sample-value').each((function(_this) {
- return function(_index, element) {
- current_value = parseFloat($(element).data("value")) + 1;
- if(isNaN(current_value)) {
- return current_value
- } else {
- $(element).val($(element).data("zscore"));
- return $(element).data("zscore");
- }
- };
- })(this));
+ current_value = this_node.value;
+ zscore_value = this_node.attributes['data-zscore'].value;
+ if(!isNaN(current_value)) {
+ this_node.value = zscore_value;
+ }
};
-check_for_zero_to_one_vals = function() {
- zero_to_one_vals_exist = false
- $('.trait-value-input').each(function() {
- current_value = $(this).data("value")
- if(isNaN(current_value)) {
- return true;
- } else {
- current_value = parseFloat(current_value)
- if (0 <= current_value && current_value < 1){
- zero_to_one_vals_exist = true
- return false
+do_transform = function(transform_type) {
+ tables = ['samples_primary', 'samples_other'];
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ if ($('#' + table).length) {
+ table_api = $('#' + table).DataTable();
+ val_nodes = table_api.column(3).nodes().to$();
+ for (i = 0; i < val_nodes.length; i++) {
+ this_node = val_nodes[i].childNodes[0]
+ if (transform_type == "log2"){
+ log2_data(this_node)
+ }
+ if (transform_type == "log10"){
+ log10_data(this_node)
+ }
+ if (transform_type == "sqrt"){
+ sqrt_data(this_node)
+ }
+ if (transform_type == "invert"){
+ invert_data(this_node)
+ }
+ if (transform_type == "qnorm"){
+ qnorm_data(this_node)
+ }
+ if (transform_type == "zscore"){
+ zscore_data(this_node)
+ }
}
}
- });
- return zero_to_one_vals_exist
+ }
}
normalize_data = function() {
if ($('#norm_method option:selected').val() == 'log2' || $('#norm_method option:selected').val() == 'log10'){
if ($('input[name="transform"]').val() != "log2" && $('#norm_method option:selected').val() == 'log2') {
- log2_normalize_data(zero_to_one_vals_exist)
+ do_transform("log2")
$('input[name="transform"]').val("log2")
- $('span[name="transform_text"]').text(" - log2 transformed")
+ $('span[name="transform_text"]').text(" - log2 Transformed")
} else {
if ($('input[name="transform"]').val() != "log10" && $('#norm_method option:selected').val() == 'log10'){
- log10_normalize_data(zero_to_one_vals_exist)
+ do_transform("log10")
$('input[name="transform"]').val("log10")
- $('span[name="transform_text"]').text(" - log10 transformed")
+ $('span[name="transform_text"]').text(" - log10 Transformed")
}
}
}
else if ($('#norm_method option:selected').val() == 'sqrt'){
if ($('input[name="transform"]').val() != "sqrt") {
- sqrt_normalize_data()
+ do_transform("sqrt")
$('input[name="transform"]').val("sqrt")
- $('span[name="transform_text"]').text(" - Square Root transformed")
+ $('span[name="transform_text"]').text(" - Square Root Transformed")
}
}
else if ($('#norm_method option:selected').val() == 'invert'){
- invert_data()
+ do_transform("invert")
$('input[name="transform"]').val("inverted")
- $('span[name="transform_text"]').text(" - Inverted")
+ if ($('span[name="transform_text"]:eq(0)').text() != ""){
+ current_text = $('span[name="transform_text"]:eq(0)').text();
+ $('span[name="transform_text"]').text(current_text + " and Inverted");
+ } else {
+ $('span[name="transform_text"]').text(" - Inverted")
+ }
}
else if ($('#norm_method option:selected').val() == 'qnorm'){
if ($('input[name="transform"]').val() != "qnorm") {
- qnorm_data()
+ do_transform("qnorm")
$('input[name="transform"]').val("qnorm")
$('span[name="transform_text"]').text(" - Quantile Normalized")
}
}
else if ($('#norm_method option:selected').val() == 'zscore'){
if ($('input[name="transform"]').val() != "zscore") {
- zscore_data()
+ do_transform("zscore")
$('input[name="transform"]').val("zscore")
$('span[name="transform_text"]').text(" - Z-Scores")
}
}
}
-zero_to_one_vals_exist = false
+zero_to_one_vals_exist = check_for_zero_to_one_vals();
show_transform_warning = function() {
transform_type = $('#norm_method option:selected').val()
- zero_to_one_vals_exist = check_for_zero_to_one_vals();
if (transform_type == "log2" || transform_type == "log10"){
if (zero_to_one_vals_exist){
$('#transform_alert').css("display", "block")
@@ -859,10 +897,9 @@ get_sample_table_data = function(table_name) {
if ($(element).find('.edit_sample_num_cases').length > 0) {
row_data.num_cases = $(element).find('.edit_sample_num_cases').val();
}
- _ref = js_data.attribute_names;
- for (key in _ref) {
- if (!__hasProp.call(_ref, key)) continue;
- attribute_info = _ref[key];
+ attr_keys = Object.keys(js_data.attributes).sort()
+ for (i=0; i < attr_keys.length; i++) {
+ attribute_info = js_data.attributes[attr_keys[i]];
row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_").replace("/", "\\/")).text());
}
return samples.push(row_data);
@@ -1447,8 +1484,11 @@ $('.stats_panel').click(function() {
edit_data_change();
}
});
-$('#edit_sample_lists').change(edit_data_change);
-$('#block_by_index').click(edit_data_change);
+
+$('#block_by_index').click(function(){
+ block_by_index();
+ edit_data_change();
+});
$('#exclude_group').click(edit_data_change);
$('#block_outliers').click(edit_data_change);
$('#reset').click(edit_data_change);
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 a48cfdaa..c0f36eaa 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,307 +1,298 @@
-// Generated by CoffeeScript 1.8.0
-(function() {
- var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
+var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
- submit_special = function(url) {
- $("#trait_data_form").attr("action", url);
- $("#trait_data_form").submit();
- };
-
- update_time_remaining = function(percent_complete) {
- var minutes_remaining, now, period, total_seconds_remaining;
- now = new Date();
- period = now.getTime() - root.start_time;
- console.log("period is:", period);
- if (period > 8000) {
- total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
- minutes_remaining = Math.round(total_seconds_remaining / 60);
- if (minutes_remaining < 3) {
- return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
- } else {
- return $('#time_remaining').text(minutes_remaining + " minutes remaining");
- }
+update_time_remaining = function(percent_complete) {
+ var minutes_remaining, now, period, total_seconds_remaining;
+ now = new Date();
+ period = now.getTime() - root.start_time;
+ console.log("period is:", period);
+ if (period > 8000) {
+ total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
+ minutes_remaining = Math.round(total_seconds_remaining / 60);
+ if (minutes_remaining < 3) {
+ return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
+ } else {
+ return $('#time_remaining').text(minutes_remaining + " minutes remaining");
}
- };
+ }
+};
- get_progress = function() {
- var params, params_str, temp_uuid, url;
- console.log("temp_uuid:", $("#temp_uuid").val());
- temp_uuid = $("#temp_uuid").val();
- params = {
- key: temp_uuid
- };
- params_str = $.param(params);
- url = "/get_temp_data?" + params_str;
- console.log("url:", url);
- $.ajax({
- type: "GET",
- url: url,
- success: (function(_this) {
- return function(progress_data) {
- var percent_complete;
- percent_complete = progress_data['percent_complete'];
- console.log("in get_progress data:", progress_data);
- $('#marker_regression_progress').css("width", percent_complete + "%");
- if (root.start_time) {
- if (!isNaN(percent_complete)) {
- return update_time_remaining(percent_complete);
- }
- } else {
- return root.start_time = new Date().getTime();
- }
- };
- })(this)
- });
- return false;
+get_progress = function() {
+ var params, params_str, temp_uuid, url;
+ console.log("temp_uuid:", $("#temp_uuid").val());
+ temp_uuid = $("#temp_uuid").val();
+ params = {
+ key: temp_uuid
};
-
- block_outliers = function() {
- return $('.outlier').each((function(_this) {
- return function(_index, element) {
- return $(element).find('.trait-value-input').val('x');
+ params_str = $.param(params);
+ url = "/get_temp_data?" + params_str;
+ console.log("url:", url);
+ $.ajax({
+ type: "GET",
+ url: url,
+ success: (function(_this) {
+ return function(progress_data) {
+ var percent_complete;
+ percent_complete = progress_data['percent_complete'];
+ console.log("in get_progress data:", progress_data);
+ $('#marker_regression_progress').css("width", percent_complete + "%");
+ if (root.start_time) {
+ if (!isNaN(percent_complete)) {
+ return update_time_remaining(percent_complete);
+ }
+ } else {
+ return root.start_time = new Date().getTime();
+ }
};
- })(this));
- };
-
- do_ajax_post = function(url, form_data) {
- $.ajax({
- type: "POST",
- url: url,
- data: form_data,
- error: (function(_this) {
- return function(xhr, ajaxOptions, thrownError) {
- alert("Sorry, an error occurred");
- console.log(xhr);
- clearInterval(_this.my_timer);
- $('#progress_bar_container').modal('hide');
- $('#static_progress_bar_container').modal('hide');
- return $("body").html("We got an error.");
- };
- })(this),
- success: (function(_this) {
- return function(data) {
- clearInterval(_this.my_timer);
- $('#progress_bar_container').modal('hide');
- $('#static_progress_bar_container').modal('hide');
- return open_mapping_results(data);
- };
- })(this)
- });
- console.log("settingInterval");
- this.my_timer = setInterval(get_progress, 1000);
- return false;
- };
-
- open_mapping_results = function(data) {
- return $.colorbox({
- html: data,
- href: "#mapping_results_holder",
- height: "90%",
- width: "90%",
- onComplete: (function(_this) {
- return function() {
- var filename, getSvgXml;
- root.create_lod_chart();
- filename = "lod_chart_" + js_data.this_trait;
- getSvgXml = function() {
- var svg;
- svg = $("#topchart").find("svg")[0];
- return (new XMLSerializer).serializeToString(svg);
- };
- $("#exportform > #export").click(function() {
- var form, svg_xml;
- svg_xml = getSvgXml();
- form = $("#exportform");
- form.find("#data").val(svg_xml);
- form.find("#filename").val(filename);
- return form.submit();
- });
- return $("#exportpdfform > #export_pdf").click(function() {
- var form, svg_xml;
- svg_xml = getSvgXml();
- form = $("#exportpdfform");
- form.find("#data").val(svg_xml);
- form.find("#filename").val(filename);
- return form.submit();
- });
- };
- })(this)
- });
- };
-
- outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results.";
- showalert = function(message, alerttype) {
- return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
- };
-
- $('#suggestive').hide();
+ })(this)
+ });
+ return false;
+};
- $('input[name=display_all]').change((function(_this) {
- return function() {
- console.log("check");
- if ($('input[name=display_all]:checked').val() === "False") {
- return $('#suggestive').show();
- } else {
- return $('#suggestive').hide();
- }
+block_outliers = function() {
+ return $('.outlier').each((function(_this) {
+ return function(_index, element) {
+ return $(element).find('.trait_value_input').val('x');
};
})(this));
+};
- //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
- var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
- 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
- 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
- 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
- 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
-
- $(".rqtl-tab, #rqtl_geno_compute").on("click", (function(_this) {
- return function() {
- if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){
- var form_data, url;
- url = "/loading";
- $('input[name=method]').val("rqtl_geno");
- $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
- $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
- $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
- $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
- $('input[name=categorical_vars]').val(js_data.categorical_vars)
- $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
- $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
- $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
- $('input[name=tool_used]').val("Mapping");
- $('input[name=form_url]').val("/run_mapping");
- $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
- return submit_special(url);
- } else {
- return true
- }
- };
- })(this));
-
- $(".gemma-tab, #gemma_compute").on("click", (function(_this) {
- return function() {
- if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){
- var form_data, url;
- console.log("RUNNING GEMMA");
- url = "/loading";
- $('input[name=method]').val("gemma");
- $('input[name=selected_chr]').val($('#chr_gemma').val());
- $('input[name=num_perm]').val(0);
- $('input[name=genofile]').val($('#genofile_gemma').val());
- $('input[name=maf]').val($('input[name=maf_gemma]').val());
- $('input[name=tool_used]').val("Mapping");
- $('input[name=form_url]').val("/run_mapping");
- $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
- return submit_special(url);
- } else {
- return true
- }
- };
- })(this));
+do_ajax_post = function(url, form_data) {
+ $.ajax({
+ type: "POST",
+ url: url,
+ data: form_data,
+ error: (function(_this) {
+ return function(xhr, ajaxOptions, thrownError) {
+ alert("Sorry, an error occurred");
+ console.log(xhr);
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ $('#static_progress_bar_container').modal('hide');
+ return $("body").html("We got an error.");
+ };
+ })(this),
+ success: (function(_this) {
+ return function(data) {
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ $('#static_progress_bar_container').modal('hide');
+ return open_mapping_results(data);
+ };
+ })(this)
+ });
+ console.log("settingInterval");
+ this.my_timer = setInterval(get_progress, 1000);
+ return false;
+};
- $(".reaper-tab, #interval_mapping_compute").on("click", (function(_this) {
- return function() {
- if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){
- var form_data, url;
- console.log("In interval mapping");
- url = "/loading";
- $('input[name=method]').val("reaper");
- $('input[name=selected_chr]').val($('#chr_reaper').val());
- $('input[name=mapping_scale]').val($('#scale_reaper').val());
- $('input[name=genofile]').val($('#genofile_reaper').val());
- $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
- $('input[name=control_marker]').val($('input[name=control_reaper]').val());
- $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
- $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
- $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
- $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
- $('input[name=tool_used]').val("Mapping");
- $('input[name=form_url]').val("/run_mapping");
- $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
- return submit_special(url);
- } else {
- return true
- }
- };
- })(this));
+open_mapping_results = function(data) {
+ return $.colorbox({
+ html: data,
+ href: "#mapping_results_holder",
+ height: "90%",
+ width: "90%",
+ onComplete: (function(_this) {
+ return function() {
+ var filename, getSvgXml;
+ root.create_lod_chart();
+ filename = "lod_chart_" + js_data.this_trait;
+ getSvgXml = function() {
+ var svg;
+ svg = $("#topchart").find("svg")[0];
+ return (new XMLSerializer).serializeToString(svg);
+ };
+ $("#exportform > #export").click(function() {
+ var form, svg_xml;
+ svg_xml = getSvgXml();
+ form = $("#exportform");
+ form.find("#data").val(svg_xml);
+ form.find("#filename").val(filename);
+ return form.submit();
+ });
+ return $("#exportpdfform > #export_pdf").click(function() {
+ var form, svg_xml;
+ svg_xml = getSvgXml();
+ form = $("#exportpdfform");
+ form.find("#data").val(svg_xml);
+ form.find("#filename").val(filename);
+ return form.submit();
+ });
+ };
+ })(this)
+ });
+};
- $("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) {
- return function() {
- if ($(".outlier").length && $(".outlier-alert").length < 1) {
- return showalert(outlier_text, "alert-success outlier-alert");
- }
- };
- })(this));
+outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results.";
+showalert = function(message, alerttype) {
+ return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
+};
- composite_mapping_fields = function() {
- return $(".composite_fields").toggle();
- };
+$('#suggestive').hide();
- mapping_method_fields = function() {
- return $(".mapping_method_fields").toggle();
+$('input[name=display_all]').change((function(_this) {
+ return function() {
+ console.log("check");
+ if ($('input[name=display_all]:checked').val() === "False") {
+ return $('#suggestive').show();
+ } else {
+ return $('#suggestive').hide();
+ }
};
+})(this));
- $("#use_composite_choice").change(composite_mapping_fields);
-
- $("#mapping_method_choice").change(mapping_method_fields);
+//ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
+var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+ 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
+ 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
+ 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
+ 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
- $("#mapmodel_rqtl_geno").change(function() {
- if ($(this).val() == "np"){
- $("#mapmethod_rqtl_geno").attr('disabled', 'disabled');
- $("#mapmethod_rqtl_geno").css('background-color', '#CCC');
- $("#missing_geno").attr('disabled', 'disabled');
- $("#missing_geno").css('background-color', '#CCC');
+$(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) {
+ return function() {
+ if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){
+ var form_data, url;
+ url = "/loading";
+ $('input[name=method]').val("rqtl_geno");
+ $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
+ $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
+ $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
+ $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
+ $('input[name=categorical_vars]').val(js_data.categorical_vars)
+ $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
+ $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
+ $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
+ $('input[name=tool_used]').val("Mapping");
+ $('input[name=form_url]').val("/run_mapping");
+ $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+ return submit_special(url);
} else {
- $("#mapmethod_rqtl_geno").removeAttr('disabled');
- $("#mapmethod_rqtl_geno").css('background-color', '#FFF');
- $("#missing_geno").removeAttr('disabled');
- $("#missing_geno").css('background-color', '#FFF');
+ return true
}
- });
+ };
+})(this));
- $("#mapmethod_rqtl_geno").change(function() {
- if ($(this).val() == "mr"){
- $("#missing_geno_div").css('display', 'block');
+$(".gemma_tab, #gemma_compute").on("click", (function(_this) {
+ return function() {
+ if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){
+ var form_data, url;
+ console.log("RUNNING GEMMA");
+ url = "/loading";
+ $('input[name=method]').val("gemma");
+ $('input[name=selected_chr]').val($('#chr_gemma').val());
+ $('input[name=num_perm]').val(0);
+ $('input[name=genofile]').val($('#genofile_gemma').val());
+ $('input[name=maf]').val($('input[name=maf_gemma]').val());
+ $('input[name=tool_used]').val("Mapping");
+ $('input[name=form_url]').val("/run_mapping");
+ $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+ return submit_special(url);
} else {
- $("#missing_geno_div").css('display', 'none');
+ return true
}
- });
+ };
+})(this));
- $("li.mapping-tab").click(function() {
- if ($(this).hasClass("rqtl-geno-tab")){
- $(".rqtl-description").css("display", "block");
+$(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) {
+ return function() {
+ if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){
+ var form_data, url;
+ console.log("In interval mapping");
+ url = "/loading";
+ $('input[name=method]').val("reaper");
+ $('input[name=selected_chr]').val($('#chr_reaper').val());
+ $('input[name=mapping_scale]').val($('#scale_reaper').val());
+ $('input[name=genofile]').val($('#genofile_reaper').val());
+ $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
+ $('input[name=control_marker]').val($('input[name=control_reaper]').val());
+ $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
+ $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
+ $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
+ $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
+ $('input[name=tool_used]').val("Mapping");
+ $('input[name=form_url]').val("/run_mapping");
+ $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+ return submit_special(url);
} else {
- $(".rqtl-description").css("display", "none");
+ return true
}
- });
+ };
+})(this));
- toggle_enable_disable = function(elem) {
- return $(elem).prop("disabled", !$(elem).prop("disabled"));
+$("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) {
+ return function() {
+ if ($(".outlier").length && $(".outlier-alert").length < 1) {
+ return showalert(outlier_text, "alert-success outlier-alert");
+ }
};
+})(this));
- $("#choose_closet_control").change(function() {
- return toggle_enable_disable("#control_locus");
- });
+composite_mapping_fields = function() {
+ return $(".composite_fields").toggle();
+};
- $("#display_all_lrs").change(function() {
- return toggle_enable_disable("#suggestive_lrs");
- });
+mapping_method_fields = function() {
+ return $(".mapping_method_fields").toggle();
+};
- $('#genofile_rqtl_geno').change(function() {
- geno_location = $(this).children("option:selected").val().split(":")[0]
- $('#scale_rqtl_geno').empty()
- the_scales = js_data.scales_in_geno[geno_location]
- for (var i = 0; i < the_scales.length; i++){
- $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
- }
- });
- $('#genofile_reaper').change(function() {
- geno_location = $(this).children("option:selected").val().split(":")[0]
- $('#scale_reaper').empty()
- the_scales = js_data.scales_in_geno[geno_location]
- for (var i = 0; i < the_scales.length; i++){
- $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
- }
- });
+$("#use_composite_choice").change(composite_mapping_fields);
+
+$("#mapping_method_choice").change(mapping_method_fields);
+
+$("#mapmodel_rqtl_geno").change(function() {
+ if ($(this).val() == "np"){
+ $("#mapmethod_rqtl_geno").attr('disabled', 'disabled');
+ $("#mapmethod_rqtl_geno").css('background-color', '#CCC');
+ $("#missing_geno").attr('disabled', 'disabled');
+ $("#missing_geno").css('background-color', '#CCC');
+ } else {
+ $("#mapmethod_rqtl_geno").removeAttr('disabled');
+ $("#mapmethod_rqtl_geno").css('background-color', '#FFF');
+ $("#missing_geno").removeAttr('disabled');
+ $("#missing_geno").css('background-color', '#FFF');
+ }
+});
+
+$("#mapmethod_rqtl_geno").change(function() {
+ if ($(this).val() == "mr"){
+ $("#missing_geno_div").css('display', 'block');
+ } else {
+ $("#missing_geno_div").css('display', 'none');
+ }
+});
+
+$("li.mapping_tab").click(function() {
+ if ($(this).hasClass("rqtl")){
+ $(".rqtl_description").css("display", "block");
+ } else {
+ $(".rqtl_description").css("display", "none");
+ }
+});
+
+toggle_enable_disable = function(elem) {
+ return $(elem).prop("disabled", !$(elem).prop("disabled"));
+};
+
+$("#choose_closet_control").change(function() {
+ return toggle_enable_disable("#control_locus");
+});
+
+$("#display_all_lrs").change(function() {
+ return toggle_enable_disable("#suggestive_lrs");
+});
-}).call(this);
+$('#genofile_rqtl_geno').change(function() {
+ geno_location = $(this).children("option:selected").val().split(":")[0]
+ $('#scale_rqtl_geno').empty()
+ the_scales = js_data.scales_in_geno[geno_location]
+ for (var i = 0; i < the_scales.length; i++){
+ $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+ }
+});
+$('#genofile_reaper').change(function() {
+ geno_location = $(this).children("option:selected").val().split(":")[0]
+ $('#scale_reaper').empty()
+ the_scales = js_data.scales_in_geno[geno_location]
+ for (var i = 0; i < the_scales.length; i++){
+ $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+ }
+});
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 52a23665..7b74a3f6 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -143,15 +143,18 @@
<script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script>
<script type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.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>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+ <script type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
+
+ <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.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>
+ <script type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
<script type="text/javascript" charset="utf-8">
@@ -208,154 +211,6 @@
}
});
- //ZS: This variable is just created to get the column position of the first case attribute, since it's needed to set the row classes in createdRow for the DataTable
- {% if sample_groups[0].attributes|length > 0 %}
- {% if sample_groups[0].se_exists() %}
- {% if has_num_cases %}
- attribute_start_pos = 6
- {% else %}
- attribute_start_pos = 5
- {% endif %}
- {% else %}
- {% if has_num_cases %}
- attribute_start_pos = 4
- {% else %}
- attribute_start_pos = 3
- {% endif %}
- {% endif %}
- {% endif %}
-
- var primary_table = $('#samples_primary').DataTable( {
- 'initComplete': function(settings, json) {
- $('.edit-sample-value').change(function() {
- edit_data_change();
- });
- },
- 'createdRow': function ( row, data, index ) {
- $(row).attr('id', "Primary_" + data.this_id)
- $(row).addClass("value_se");
- if (data.outlier) {
- $(row).addClass("outlier");
- }
- $('td', row).eq(0).addClass("column_name-Checkbox")
- $('td', row).eq(1).addClass("column_name-Index")
- $('td', row).eq(2).addClass("column_name-Sample")
- $('td', row).eq(3).addClass("column_name-Value")
- {% if sample_groups[0].se_exists() %}
- $('td', row).eq(4).addClass("column_name-PlusMinus")
- $('td', row).eq(5).addClass("column_name-SE value_column")
- {% if has_num_cases %}
- $('td', row).eq(6).addClass("column_name-num_cases")
- {% endif %} {% else %} {% if has_num_cases %}
- $('td', row).eq(4).addClass("column_name-num_cases")
- {% endif %} {% endif %}
- {% if sample_groups[0].attributes|length > 0 %}
- {% for attribute in sample_groups[0].attributes|sort() %}
- $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[0].attributes[attribute].name }}")
- $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[0].attributes[attribute].alignment }};")
- {% endfor %}
- {% endif %}
- },
- 'data': js_data['sample_lists'][0],
- 'columns': [
- {
- 'data': null,
- 'orderDataType': "dom-checkbox",
- 'searchable' : false,
- 'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="searchResult" class="checkbox edit_sample_checkbox" value="">'
- }
- },
- {
- 'title': "ID",
- 'type': "natural",
- 'searchable' : false,
- 'data': "this_id"
- },
- {
- 'title': "Sample",
- 'type': "natural",
- 'data': null,
- 'render': function(data, type, row, meta) {
- return '<span class="edit-sample-sample-name">' + data.name + '</span>'
- }
- },
- {
- 'title': "<div class='numeric_header'>Value</div>",
- 'orderDataType': "dom-input",
- 'type': "cust-txt",
- 'data': null,
- 'render': function(data, type, row, meta) {
- if (data.value == null) {
- return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait-value-input edit-sample-value" value="x" size=6 maxlength=6>'
- } else {
- return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" class="trait-value-input edit-sample-value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
- }
- }
- }{% if sample_groups[0].se_exists() %},
- {
- 'bSortable': false,
- 'type': "natural",
- 'data': null,
- 'searchable' : false,
- 'render': function(data, type, row, meta) {
- return '±'
- }
- },
- {
- 'title': "<div class='numeric_header'>SE</div>",
- 'orderDataType': "dom-input",
- 'type': "cust-txt",
- 'data': null,
- 'render': function(data, type, row, meta) {
- if (data.variance == null) {
- return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait-value-input edit_sample_se" value="x" size=6 maxlength=6>'
- } else {
- return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait-value-input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
- }
- }
- }{% endif %}{% if has_num_cases %},
- {
- 'title': "<div class='numeric_header'>N</div>",
- 'orderDataType': "dom-input",
- 'type': "cust-txt",
- 'data': null,
- 'render': function(data, type, row, meta) {
- if (data.num_cases == null || data.num_cases == undefined) {
- return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait-value-input edit_sample_num_cases" value="x" size=4 maxlength=4>'
- } else {
- return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait-value-input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
- }
- }
- }{% endif %}{% if sample_groups[0].attributes|length > 0 %}{% for attribute in sample_groups[0].attributes|sort() %},
- {
- 'title': "<div style='text-align: {{ sample_groups[0].attributes[attribute].alignment }}'>{{ sample_groups[0].attributes[attribute].name }}</div>",
- 'type': "natural",
- 'data': null,
- 'render': function(data, type, row, meta) {
- if (data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] != null && data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] != undefined){
- return data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}']
- } else {
- return ""
- }
- }
- }{% endfor %}{% endif %}
- ],
- 'order': [[1, "asc"]],
- 'sDom': "Ztr",
- 'autoWidth': true,
- 'deferRender': true,
- 'paging': false,
- 'orderClasses': true,
- 'scrollY': "600px",
- 'scrollCollapse': false,
- 'processing': true,
- 'language': {
- 'loadingRecords': '&nbsp;',
- 'processing': 'Loading...'
- }
- } );
-
primary_table.on( 'order.dt search.dt draw.dt', function () {
primary_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) {
cell.innerHTML = i+1;
@@ -367,136 +222,6 @@
} );
{% if sample_groups|length != 1 %}
- var other_table = $('#samples_other').DataTable( {
- 'initComplete': function(settings, json) {
- $('.edit-sample-value').change(function() {
- edit_data_change();
- });
- },
- 'createdRow': function ( row, data, index ) {
- $(row).attr('id', "Other_" + data.this_id)
- $(row).addClass("value_se");
- if (data.outlier) {
- $(row).addClass("outlier");
- }
- $('td', row).eq(1).addClass("column_name-Index")
- $('td', row).eq(2).addClass("column_name-Sample")
- $('td', row).eq(3).addClass("column_name-Value")
- {% if sample_groups[1].se_exists() %}
- $('td', row).eq(4).addClass("column_name-PlusMinus")
- $('td', row).eq(5).addClass("column_name-SE")
- {% if has_num_cases %}
- $('td', row).eq(6).addClass("column_name-num_cases")
- {% endif %} {% else %} {% if has_num_cases %}
- $('td', row).eq(4).addClass("column_name-num_cases")
- {% endif %} {% endif %}
- {% if sample_groups[1].attributes|length > 0 %}
- {% for attribute in sample_groups[1].attributes|sort() %}
- $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[1].attributes[attribute].name }}")
- $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[1].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;")
- {% endfor %}
- {% endif %}
- },
- 'data': js_data['sample_lists'][1],
- 'columns': [
- {
- 'data': null,
- 'orderDataType': "dom-checkbox",
- 'searchable' : false,
- 'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="searchResult" class="checkbox edit_sample_checkbox" value="">'
- }
- },
- {
- 'title': "ID",
- 'type': "natural",
- 'data': "this_id",
- 'searchable' : false
- },
- {
- 'title': "Sample",
- 'type': "natural",
- 'data': null,
- 'render': function(data, type, row, meta) {
- return '<span class="edit-sample-sample-name">' + data.name + '</span>'
- }
- },
- {
- 'title': "<div class='numeric_header'>Value</div>",
- 'orderDataType': "dom-input",
- 'type': "cust-txt",
- 'data': null,
- 'render': function(data, type, row, meta) {
- if (data.value == null) {
- return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" class="trait-value-input edit-sample-value" value="x" size=6 maxlength=6>'
- } else {
- return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][1][parseInt(data.this_id)] + '" name="value:' + data.name + '" class="trait-value-input edit-sample-value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
- }
- }
- }{% if sample_groups[1].se_exists() %},
- {
- 'bSortable': false,
- 'type': "natural",
- 'data': null,
- 'searchable' : false,
- 'render': function(data, type, row, meta) {
- return '±'
- }
- },
- {
- 'title': "<div class='numeric_header'>SE</div>",
- 'orderDataType': "dom-input",
- 'type': "cust-txt",
- 'data': null,
- 'render': function(data, type, row, meta) {
- if (data.variance == null) {
- return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" class="trait-value-input edit_sample_se" value="x" size=6 maxlength=6>'
- } else {
- return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" name="value:' + data.name + '" class="trait-value-input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
- }
- }
- }{% endif %}{% if has_num_cases %},
- {
- 'title': "<div class='numeric_header'>N</div>",
- 'orderDataType': "dom-input",
- 'type': "cust-txt",
- 'data': null,
- 'render': function(data, type, row, meta) {
- if (data.num_cases == null) {
- return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" class="trait-value-input edit_sample_num_cases" value="x" size=4 maxlength=4>'
- } else {
- return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" name="value:' + data.name + '" class="trait-value-input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
- }
- }
- }{% endif %}{% if sample_groups[1].attributes|length > 0 %}{% for attribute in sample_groups[1].attributes|sort() %},
- {
- 'title': "<div style='text-align: {{ sample_groups[1].attributes[attribute].alignment }}'>{{ sample_groups[1].attributes[attribute].name }}</div>",
- 'type': "natural",
- 'data': null,
- 'render': function(data, type, row, meta) {
- if (data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] != null && data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] != undefined){
- return data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}']
- } else {
- return ""
- }
- }
- }{% endfor %}{% endif %}
- ],
- 'order': [[1, "asc"]],
- 'sDom': "Ztr",
- 'autoWidth': true,
- 'deferRender': true,
- 'paging': false,
- 'orderClasses': true,
- 'scrollY': "600px",
- 'scrollCollapse': false,
- 'processing': true,
- 'language': {
- 'loadingRecords': '&nbsp;',
- 'processing': 'Loading...'
- }
- } );
-
$('#other_searchbox').on( 'keyup', function () {
other_table.search($(this).val()).draw();
} );
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 3956a34f..9946c25b 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -1,9 +1,9 @@
<div>
- <div class="form-horizontal">
- <p>Edit or delete values in the Trait Data boxes, and use the
- <strong>Reset</strong> option as
- needed.
- </p>
+ <div class="form-horizontal">
+ <p>Edit or delete values in the Trait Data boxes, and use the
+ <strong>Reset</strong> option as
+ needed.
+ </p>
<div id="blockMenuSpan" class="input-append block-by-index-div">
<label for="remove_samples_field">Block samples by index:</label>
@@ -53,10 +53,10 @@
{% if negative_vals_exist == "false" %}
<option value="log2">Log2</option>
<option value="log10">Log10</option>
+ <option value="sqrt">Square Root</option>
{% endif %}
<option value="zscore">Z-score</option>
<option value="qnorm">Quantile</option>
- <option value="sqrt">Square Root</option>
<option value="invert">Invert +/-</option>
</select>
</div>
@@ -64,20 +64,24 @@
{% if sample_groups[0].sample_qnorm is not none %}
<input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
{% endif %}
- -->
+ <option value="zscore">Z-score</option>
+ <option value="qnorm">Quantile</option>
+ <option value="invert">Invert +/-</option>
+ </select>
</div>
- <br>
+ </div>
+ <br>
- <div>
- <p>Outliers highlighted in
- <strong style="background-color:orange;">orange</strong>
- can be hidden using
- the <strong>Hide Outliers</strong> button.
- </p>
+ <div>
+ <p>Outliers highlighted in
+ <strong style="background-color:orange;">orange</strong>
+ can be hidden using
+ the <strong>Hide Outliers</strong> button.
+ </p>
- <p>Samples with no value (x) can be hidden by clicking
- <strong>Hide No Value</strong> button.
- </p>
- </div>
- </div>
+ <p>Samples with no value (x) can be hidden by clicking
+ <strong>Hide No Value</strong> button.
+ </p>
+ </div>
+ </div>
</div> \ No newline at end of file
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 08:17:25 +0000