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new_results_page.jinja2
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new_results_page.jinja2
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{% extends "sitebase.jinja2" %}
{% set page_title = _("Sample Report") %}
{% set show_breadcrumbs = show_breadcrumbs %}
{% block head %}
<link rel="stylesheet" type="text/css" href="/static/vendor/css/jquery.dataTables.css" />
<link id="emperor-css" rel="stylesheet" type="text/css" href="/static/vendor/emperor/css/emperor.css">
<link rel="stylesheet" type="text/css" href="/static/vendor/emperor/vendor/css/jquery-ui.min.css">
<link rel="stylesheet" type="text/css" href="/static/vendor/emperor/vendor/css/slick.grid.min.css">
<link rel="stylesheet" type="text/css" href="/static/vendor/emperor/vendor/css/spectrum.min.css">
<link rel="stylesheet" type="text/css" href="/static/vendor/emperor/vendor/css/chosen.min.css">
<link rel="stylesheet" type="text/css" href="/static/vendor/emperor/vendor/css/jquery.contextMenu.min.css">
<link rel="stylesheet" type="text/css" href="/static/css/4_column_flex.css" />
<style>
.nav-white-bg {
background-color: #fff;
width: auto;
}
.diversity-icon {
vertical-align: middle;
width: 72px;
height: 72px;
object-fit: contain;
float:left;
}
.diversity-text {
vertical-align:middle;
display:inline;
float:left;
padding: 10px;
padding-left: 20px;
}
.diversity-header {
background-color: #EDECEF;
padding: 10px;
}
.diversity-compare {
background-color: #ffffff;
color: #747678;
border-radius: 15px;
padding: 10px;
padding-left: 20px;
border-style: solid;
border-width: 2px;
border-color: #006a96;
width: 30%;
margin: 20px;
}
.diversity-category {
color: #006a96;
}
.diversity-info {
}
.diversity-banner {
width: 100%;
max-width: 1920px;
height: auto;
border-radius: 8px;
border: 1px solid #ddd;
}
.similarity-fontstyle-same {
color: var(--ucsd-green);
}
.similarity-fontstyle-different {
color: var(--ucsd-brown);
}
/*.micromap {
min-width: 400px;
min-height: 300px;
}*/
.microinfo {
min-width: 40%;
}
/*Removes the .active, .accordion:hover effect from minimal_interface.css*/
/* Could potentially use color: initial but has less support...? */
.accordion-microbiome-map
{
background-color: #eee;
color: #000;
cursor: pointer;
padding: 5px;
width: 100%;
text-align: left;
border: none;
outline: none;
transition: 0.4s;
margin-bottom: 1%;
margin-top: 1%;
}
.accordion-panel-microbiome-map {
background-color: white;
max-height: 0;
overflow: hidden;
transition: max-height 0.2s ease-out;
}
.tab-pane {
background-color: #FFFFFF;
color: #000000;
}
.microbe-count {
font-weight: bold;
}
div.results_text {
text-align: left;
}
div.how_you_compare_section {
background-color: #f1f1f1;
color: #747678;
border-radius: 15px;
padding: 10px;
padding-left: 20px;
border-style: solid;
border-width: thin;
border-color: #006a96;
width: 70%;
}
div.how_you_compare_section h3 {
color: #006a96;
font-weight: lighter;
font-family: Mulish,sans-serif;
font-size: 36px;
}
div.how_you_compare_section h4 {
color: #006a96;
font-weight: lighter;
font-family: Mulish,sans-serif;
font-size: 20px;
}
div.how_you_compare_section p {
font: normal normal 400 14px/1.6 Muli,sans-serif;
font-variant-numeric: oldstyle-nums;
color: #747678;
}
div.how_you_compare_section a {
color: #006a96;
}
div.your_sample_diversity_inset {
background-color: #006a96;
color: #ffffff;
font-size: 20px;
border-radius: 15px;
border-style: solid;
border-width: thin;
border-color: #006a96;
width: 35%;
box-shadow: 0 4px 8px 0 rgb(0 0 0 / 20%), 0 6px 20px 0 rgb(0 0 0 / 19%);
}
.scatter-bg {
background-image: url('/static/img/scatter.png');
background: url('/static/img/scatter.png');
background-position: top 400px left 0px;
background-size: 220px;
background-origin: content-box;
background-repeat: no-repeat;
}
div.your_sample_diversity_inset .card-header {
color: #ffffff;
text-align: center;
border-radius: 15px 15px 0 0;
color: #006a96;
}
div.your_sample_diversity_inset .card-body {
color: #ffffff;
font-size: 32px;
text-align: center;
}
.tooltipper {
color: #fc8900;
}
.tooltip.show {
opacity: 1;
}
.tooltip-inner {
background-color: #ffffff; !important;
color: #747678;
border: 2px solid #fc8900;
}
.bs-tooltip-auto[x-placement^=bottom] .arrow::before, .bs-tooltip-bottom .arrow::before {
border-bottom-color: #fc8900 !important;
}
.bs-tooltip-auto[x-placement^=top] .arrow::before, .bs-tooltip-top .arrow::before {
border-top-color: #fc8900 !important;
}
.bs-tooltip-auto[x-placement^=left] .arrow::before, .bs-tooltip-left .arrow::before {
border-left-color: #fc8900 !important;
}
.bs-tooltip-auto[x-placement^=right] .arrow::before, .bs-tooltip-right .arrow::before {
border-right-color: #fc8900 !important;
}
</style>
<script type="text/javascript" language="javascript" src="/static/js/ruleset.js"></script>
<!-- Datatables must precede emperor imports, they don't play nice with each other. -->
<script type="text/javascript" charset="utf8" src="/static/vendor/js/jquery.dataTables.js"></script>
<script src="/static/vendor/DataTables/Buttons-1.6.2/js/dataTables.buttons.min.js"></script>
<script src="/static/vendor/DataTables/Buttons-1.6.2/js/buttons.html5.min.js"></script>
<script src="/static/vendor/DataTables/PercentageBars-1.10.21/js/percentageBars.js"></script>
<!-- plotly must precede emperor imports as well. I'm getting the feeling
that emperor doesn't know how to play nice. -->
<script src='https://cdn.plot.ly/plotly-latest.min.js'></script>
<script src="/static/vendor/emperor/vendor/js/require-2.1.22.min.js"></script>
<script src="/static/vendor/emperor/emperor_loader.js"></script>
<script>
"use strict";
var dynamic_text_dictionary = {
"11 to 20": "{{ _('11 to 20') }}",
"21 to 30": "{{ _('21 to 30') }}",
"5-6 hours": "{{ _('5-6 hours') }}",
"6 to 10": "{{ _('6 to 10') }}",
"6-7 hours": "{{ _('6-7 hours') }}",
"7-8 hours": "{{ _('7-8 hours') }}",
"8 or more hours": "{{ _('8 or more hours') }}",
"Daily": "{{ _('Daily') }}",
"Less than 5": "{{ _('Less than 5') }}",
"Less than 5 hours": "{{ _('Less than 5 hours') }}",
"More than 30": "{{ _('More than 30') }}",
"Never": "{{ _('Never') }}",
"Not provided": "{{ _('Not provided') }}",
"Occasionally (1-2 times/week)": "{{ _('Occasionally (1-2 times/week)') }}",
"Rarely (a few times/month)": "{{ _('Rarely (a few times/month)') }}",
"Rarely (less than once/week)": "{{ _('Rarely (less than once/week)') }}",
"Regularly (3-5 times/week)": "{{ _('Regularly (3-5 times/week)') }}",
"not applicable": "{{ _('Not provided') }}",
"not collected": "{{ _('Not provided') }}",
"not provided": "{{ _('Not provided') }}"
};
function placeURLSourcedImageFromDetail(state, url, detail) {
/* this creates the following html structure off of #pcoa-div
<div id="accordion-div-id">
<button class="accordion-microbiome-map">
<h4 class="diversity-header">button_text</h4>
</button>
<div class="accordion-panel-microbiome-map" style="">
<div class="row">
<div class="col-5">
<div id="img_div_id">
<img id="imgid" src="#" alt="img" class="img-fluid"/>
</div>
</div>
<div class="col microinfo">
description
</div>
</div>
</div>
</div>
*/
var pcoa_div = document.getElementById('pcoa-div');
var img = document.createElement('img');
img.id = detail['img_id'];
img.classList.add('img-fluid');
img.setAttribute('alt', 'img');
var img_div = document.createElement('div');
img_div.id = detail['img_div_id'];
img_div.appendChild(img);
var content_div = document.createElement('div');
content_div.classList.add('accordion-panel-microbiome-map');
content_div.style = '';
var content_div_row = document.createElement('div');
content_div_row.classList.add('row');
var content_div_img = document.createElement('div');
content_div_img.classList.add('col-5');
var content_div_desc = document.createElement('div');
content_div_desc.classList.add('col');
content_div_desc.classList.add('microinfo');
content_div_desc.innerHTML = detail['description'];
content_div_img.appendChild(img_div);
content_div_row.appendChild(content_div_img);
content_div_row.appendChild(content_div_desc);
content_div.appendChild(content_div_row);
var button_text = document.createElement('h4');
button_text.classList.add('diversity-header');
button_text.innerText = detail['button_text'];
var button = document.createElement('button');
button.classList.add('accordion-microbiome-map');
button.style = '';
button.type = 'button';
button.appendChild(button_text);
var accordion = document.createElement('div')
accordion.classList.add('microbiome-map-multipop-lifestage-accordian');
accordion.appendChild(button);
accordion.appendChild(content_div);
pcoa_div.appendChild(accordion);
placeURLSourcedImage(state, url, detail['img_id']);
};
function placeURLSourcedImage(state, url, divSelector) {
$('#' + divSelector).attr('src', url);
};
var pcoa_structure = {
'tmi_16S_gut_all_samples': {
'dataset': 'tmi-16S-allsamples',
'category': 'microbial_map',
'accordion_div_id': 'microbiome-map-all-tmi-accordion',
'button_text': "{{ _('Microbiomes Across the Body') }}",
'img_div_id': 'pcoa-tmi-all-samples',
'img_id': 'pcoa-tmi-all-samples-img',
'description': "<p>{{ _('In this map, we\'ve placed your sample relative to all the other samples we have in Microsetta. As you can see, there are a few different types of samples people have contributed, and the microbial configurations present can be VERY different.') }}</p>"},
'tmi_16S_gut_multipop': {
'dataset': 'multipop-16S-gut',
'category': 'microbial_map_region',
'accordion_div_id': 'microbiome-map-multipop-region-accordion',
'button_text': "{{ _('Microbiomes Across the World') }}",
'img_div_id': 'pcoa-multipopulation-region',
'img_id': 'pcoa-multipopulation-region-img',
'description': "<p>{{ _('Researchers have noted large differences in our microbiomes depending on where we live. The reason why is not fully understood, but they suspect factors such as diet or environmental exposures (e.g. plants, pets, what\'s in your house, pollution, how often you come in contact with soil, etc) may be major factors.<br /><br />Researchers do not yet know how much these differences between locations matter, but it is a topic that is under active investigation.') }}</p>"},
'tmi_16S_gut_lifestage': {
'dataset': 'lifestage-16S-gut',
'category': 'microbial_map_lifestage',
'accordion_div_id': 'microbiome-map-multipop-lifestage-accordian',
'button_text': "{{ _('Microbiomes Across the Lifespan') }}",
'img_div_id': 'pcoa-multipopulation-lifestage',
'img_id': 'pcoa-multipopulation-lifestage-img',
'description': "<p>{{ _('One major factor associated with gut microbiomes is the age of the individual, represented in this map by life stages.<br /><br />Interestingly, compared to differences among adults living in different areas of the world, infants are relatively similar microbially regardless of where they were born. But, as individuals age, their microbiomes reflect greater geographical or lifestyle differences.') }}</p>"},
'tmi_16S_gut_builtenv': {
'dataset': 'builtenv-16S-allsamples',
'category': 'microbial_map',
'accordion_div_id': 'microbiome-map-builtenv-accordian',
'button_text': "{{ _('Microbiomes in the Environment') }}",
'img_div_id': 'pcoa-builtenv',
'img_id': 'pcoa-builtenv-img',
'description': "<p>{{ _('Microbes don\'t just live inside and on your body; they are everywhere! Using the same techniques described in the previous maps, we compared your microbiome to samples collected from all over the surfaces of brand-new hospital offices.<br /><br />As you can see, skin samples tend to more closely resemble those from \'the office surfaces,\' which makes sense as skin cells are constantly shedding from you. In an indoor environment, dust is typically composed of up to 50%% dead skin cells.') }}</p>"},
'tmi_WGS_gut_multipop': {
'dataset': 'multipop-WGS-gut',
'category': 'microbial_map_region',
'accordion_div_id': 'microbiome-map-multipop-accordian',
'button_text': "{{ _('Microbiomes Across the World') }}",
'img_div_id': 'pcoa-multipopulation-region',
'img_id': 'pcoa-multipopulation-region-img',
'description': "<p>{{ _('Researchers have noted large differences in our microbiomes depending on where we live. The reason why is not fully understood, but they suspect factors such as diet or environmental exposures (e.g. plants, pets, what\'s in your house, pollution, how often you come in contact with soil, etc) may be major factors.<br /><br />Researchers do not yet know how much these differences between locations matter, but it is a topic that is under active investigation.') }}</p>"},
'tmi_WGS_gut_lifestage': {
'dataset': 'lifestage-WGS-gut',
'category': 'microbial_map_lifestage',
'accordion_div_id': 'microbiome-map-multipop-lifestage-accordian',
'button_text': "{{ _('Microbiomes Across the Lifespan') }}",
'img_div_id': 'pcoa-multipopulation-lifestage',
'img_id': 'pcoa-multipopulation-lifestage-img',
'description': "<p>{{ _('One major factor associated with gut microbiomes is the age of the individual, represented in this map by life stages.<br /><br />Interestingly, compared to differences among adults living in different areas of the world, infants are relatively similar microbially regardless of where they were born. But, as individuals age, their microbiomes reflect greater geographical or lifestyle differences.') }}</p>"}
};
function getMicrobiomeMapsRasterizedPlots(state) {
if(state.dataset_type.value === 'WGS') {
var pcoa_plots = ['tmi_WGS_gut_multipop', 'tmi_WGS_gut_lifestage'];
} else {
var pcoa_plots = ['tmi_16S_gut_all_samples', 'tmi_16S_gut_multipop', 'tmi_16S_gut_lifestage', 'tmi_16S_gut_builtenv'];
}
for (var key of pcoa_plots) {
let detail = pcoa_structure[key];
let url = state.public_endpoint +
'/dataset/' +
detail['dataset'] +
'/plotting/diversity/beta/' +
state.beta_metric +
'/pcoa/full-dataset/' +
'png?category=' +
detail['category'] +
'&sample_id=' +
state.barcode_prefix +
state.sample_id;
placeURLSourcedImageFromDetail(state, url, detail);
}
setupAccordions();
};
function datasets_span(label_text, span_id) {
var div = document.getElementById('datasets-used');
var label = document.createElement('h5');
label.innerText = label_text;
var list = document.createElement('ul');
var span = document.createElement('span');
span.id = span_id.substring(1);
span.classList.add('info-loader');
span.classList.add('text-success');
div.appendChild(label);
div.appendChild(list);
list.appendChild(span);
div.appendChild(document.createElement('br'));
}
function addDatasetDetail(detail) {
let name = Object.keys(detail)[0];
let info = detail[name];
let span_id = "";
let label = "";
// Qiita doesn't provide an easy way to obtain this detail
// soo... not ideal but let's provide a way to get study
// links for various datasets
let study_lookup = {'10317': ["American Gut: an Open Platform for Citizen Science Microbiome Research",
"https://msystems.asm.org/content/3/3/e00031-18"],
"850": ["Human gut microbiome viewed across age and geography",
"https://www.nature.com/articles/nature11053"],
"10297": ["Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota",
"https://www.nature.com/articles/srep40466"],
"10080": ["The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia", "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288704/"],
"10300": ["The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia", "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288704/"],
"11076": ["Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk", "https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0198-6"],
"11884": ["Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability", "https://stm.sciencemag.org/content/8/343/343ra81"],
"1454": ["Persistent gut microbiota immaturity in malnourished Bangladeshi children", "https://www.nature.com/articles/nature13421"],
"10249": ["Antibiotics, birth mode, and diet shape microbiome maturation during early life", "https://stm.sciencemag.org/content/8/343/343ra82"],
"11937": ["Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort", "https://mbio.asm.org/content/9/5/e01751-18"],
"10333": ["Walls talk: Microbial biogeography of homes spanning urbanization", "https://advances.sciencemag.org/content/2/2/e1501061"],
"10423": ["Geography and location are the primary drivers of office microbiome composition", "https://msystems.asm.org/content/1/2/e00022-16"],
"11358": ["Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania", "https://science.sciencemag.org/content/357/6353/802"],
"2024": ["Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt", "https://aem.asm.org/content/81/15/4965"],
"11993": ["Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization", "https://www.nature.com/articles/s41598-018-29687-x"],
"10581": ["Cohort of human mothers and babies from El Salvador ", "https://www.ebi.ac.uk/ena/browser/view/ERP112775"],
"10352": ["Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh", "https://aem.asm.org/content/83/10/e00361-17"],
"11757": ["Regional variation limits applications of healthy gut microbiome reference ranges and disease models", "https://www.nature.com/articles/s41591-018-0164-x"],
"1481": ["Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber", "https://academic.oup.com/ajcn/article/101/2/251/4494380"],
"10052": ["The microbiome of uncontacted Amerindians", "https://advances.sciencemag.org/content/1/3/e1500183"],
"1448": ["Subsistence strategies in traditional societies distinguish gut microbiomes", "https://www.nature.com/articles/ncomms7505"],
"1718": ["Infant time series", ""],
"11666": ["Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity", "https://pubmed.ncbi.nlm.nih.gov/31672155/"],
"12142": ["The National FINRISK Study ", "https://www.nature.com/articles/s41467-021-22962-y"],
"1926": ["Structure, function and diversity of the healthy human microbiome", "https://www.nature.com/articles/nature11234"],
"11484": ["Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases", "https://pubmed.ncbi.nlm.nih.gov/31142855/"],
"11405": ["The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months ", "https://pubmed.ncbi.nlm.nih.gov/32047925/"],
"11546": ["Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity", "https://pubmed.ncbi.nlm.nih.gov/33026068/"]
}
switch (name) {
case "builtenv-16S-allsamples":
label = '{{ _('Microbiomes in the Environment') }}';
span_id = "#dataset_links_builtenv";
break;
case "tmi-WGS-gut":
case "tmi-16S-gut":
label = '{{ _('The Microsetta Initiative') }}';
span_id = "#dataset_links_tmi";
break;
case "multipop-16S-gut":
case "multipop-WGS-gut":
label = '{{ _('Microbiomes Across the World') }}';
span_id = "#dataset_links_multipopgut";
break;
case "lifestage-16S-gut":
case "lifestage-WGS-gut":
label = '{{ _('Microbiomes Across the Lifespan') }}';
span_id = "#dataset_links_lifestagegut";
break;
default:
return;
};
datasets_span(label, span_id);
let study_title = "";
let study_url = "";
let to_append = "";
for (var qiita_id of info['qiita-study-ids']) {
if(qiita_id in study_lookup) {
study_title = study_lookup[qiita_id][0];
study_url = study_lookup[qiita_id][1];
to_append = '<li><h6 style="margin-bottom: 0px;">' + study_title + '</h6>'; //<span>' + study_title + '</span>';
if(study_url !== "") {
to_append = to_append + '<a href="' + study_url + '">{{ _('Publication link') }}</a><br />';
}
to_append = to_append + '<a href="https://qiita.ucsd.edu/public/?study_id=' + qiita_id + '">{{ _('Data access (Qiita study') }} ' + qiita_id + ')</a>';
to_append = to_append + '</li>';
$(span_id).append(to_append).removeClass("spinner-grow spinner-grow-sm");
}
}
//$(span_id).append('<li><h6>' + study_title + '</h6><br /><span>' + study_title + '</span>
//$(span_id).append('<li><a href="https://qiita.ucsd.edu/public/?study_id=' + qiita_id + '">Qiita Study: ' + qiita_id + '</li>').removeClass("spinner-grow spinner-grow-sm");
//if (detail['qiita-study-ids'].length > 1)
// $("#dataset_meta_analysis").text(" (which was a meta analysis that combines the data you helped collect with other public microbiome results)").removeClass("spinner-grow spinner-grow-sm");
//else
// $("#dataset_meta_analysis").text("").removeClass("spinner-grow spinner-grow-sm")
}
function refreshDatasets(state) {
let url = state.public_endpoint + '/sample/list/dataset/' + state.barcode_prefix + state.sample_id;
$.ajax({
url: url,
type: "GET",
success: function(data)
{
var have_wgs = false;
var have_16S = false;
for (var i = 0; i < data.length; i++) {
if(data[i] === 'tmi-WGS-gut') {
have_wgs = true;
} else if(data[i] === 'tmi-16S-gut') {
have_16S = true;
}
}
if(!have_wgs && !have_16S) {
state.dataset_type.value = null
// error gracefully somehow?
} else if(have_wgs) {
// WGS samples return both WGS and 16S data sets but we only want to display WGS on the "How can I learn more?" tab
for (var i = 0; i < data.length; i++) {
if(data[i].includes("WGS")) {
$.ajax({
url: state.public_endpoint + "/dataset/" + data[i],
type: "GET",
success: function (detail) {
addDatasetDetail(detail);
}
});
}
}
state.dataset_type.value = 'WGS';
state.dataset_site.value = 'gut';
state.dataset_input.value = 'tmi-WGS-gut';
} else {
for (var i = 0; i < data.length; i++) {
$.ajax({
url: state.public_endpoint + "/dataset/" + data[i],
type: "GET",
success: function (detail) {
addDatasetDetail(detail);
}
});
}
state.dataset_type.value = '16S';
state.dataset_site.value = 'gut';
state.dataset_input.value = 'tmi-16S-gut';
}
}
});
}
function populateSelect(select_selector, value_to_text, active_value){
let select = $(select_selector);
select.empty();
for (let v in value_to_text)
{
let option = $('<option></option>')
.attr("value", v)
.text(v);
// .text(value_to_text[v]); //It should be this, but public api needs to send down friendly names
if (v === active_value)
option.attr('selected','selected');
select.append(option);
}
select.prop("disabled", false);
}
function createTaxonomyTable(state)
{
$('#taxonomyTable').DataTable(
{
destroy: true, // Necessary to replace existing datatable
language: {
url: '/static/vendor/DataTables/{{ _(EN_US_KEY) }}.json'
},
ajax: {
url: state.public_endpoint + '/dataset/' + state.dataset_input.value + "/taxonomy/present/single/" + state.taxonomy + "/" + state.barcode_prefix + state.sample_id,
dataSrc: function(d){
let representatives = {};
let generaSums = {};
//Collapse to genera (Don't show separate rows per species)
for (let i = 0; i < d.data.length; i++){
//Can't just key by genus because genus can be null/undefined. Argh.
let genus_key = d.data[i].Kingdom + ";" +
d.data[i].Phylum + ";" +
d.data[i].Class + ";" +
d.data[i].Order + ";" +
d.data[i].Family + ";" +
d.data[i].Genus;
if (genus_key in generaSums)
{
generaSums[genus_key] += d.data[i].relativeAbundance;
}
else
{
representatives[genus_key] = d.data[i];
generaSums[genus_key] = d.data[i].relativeAbundance;
}
}
let newData = [];
for (let genus_key in generaSums){
let rep = representatives[genus_key];
let sum = generaSums[genus_key];
let relativeAbundance = (sum * 100)
if (relativeAbundance <= 0.001) {
continue;
}
rep.relativeAbundance = relativeAbundance.toFixed(3);
for (var key of ["Kingdom", "Phylum", "Class", "Order", "Family", "Genus"]){
if (rep[key] != null && rep[key].startsWith("[") && rep[key].endsWith("]"))
rep[key] = rep[key].substring(1,rep[key].length-1)
}
newData.push(rep);
}
return newData;
},
},
columns: [
{
data: "relativeAbundance",
render: $.fn.dataTable.render.percentBar('round','#FFF', '#269ABC', '#31B0D5', '#286090', 3, 'groove')
},
{data: "Kingdom"},
{data: "Phylum"},
{data: "Class"},
{data: "Order"},
{data: "Family"},
{data: "Genus"},
],
order: [[ 0, "desc" ]],
dom: "Bfrtip",
buttons: [{extend: 'csv', className: 'btn btn-info', text: '{{ _('Download the spreadsheet') }}'}],
initComplete: function(settings) {
$('#taxonomyTable thead th').each(function () {
let $td = $(this);
let value = $td.text();
switch (value) {
case "{{ _('Kingdom') }}":
value = "{{ _('The broadest classification like Bacteria, Archaea and Eukaryokes (what humans are!)') }}";
break;
case "{{ _('Phylum') }}":
value = "{{ _('Within the kingdom Eukarya, this is like the difference between humans and plants') }}";
break;
case "{{ _('Class') }}":
value = "{{ _('Within the phylum Chordata, this is along the lines of humans and fish') }}";
break;
case "{{ _('Order') }}":
value = "{{ _('Within the class Mammalia, this is like the difference between whales and a dogs') }}";
break;
case "{{ _('Family') }}":
value = "{{ _('With the order Carnivora are the families for dogs and cats') }}";
break;
case "{{ _('Genus') }}":
value = "{{ _('Within the family Canidae, you would find a genus for foxes and one for wolves') }}";
break;
default:
value = "";
break;
}
$td.attr('title', value);
});
/* Apply the tooltips */
$('#taxonomyTable thead th[title]').tooltip(
{
container: 'body',
placement: 'auto'
});
}
}
);
}
function retrieveNeighbors(state, k){
let url = state.public_endpoint + '/dataset/' + state.dataset_input.value + '/diversity/beta/' + state.beta_metric + '/nearest';
return $.ajax({
method: "GET",
url: url,
data: {
sample_id: state.barcode_prefix + state.sample_id,
k:k
}
}).fail(function(result, textStatus, errorThrown){
console.log("Couldn't retrieve neighbors" + textStatus)
});
}
function fillNNResults(state, categories, chooserMap, selectorMap) {
return function(samplesQueried, sampleResults) {
// Count number of responses for each answer of each question
let categoryCounts = {}
let display = {}
for (let i = 0; i < samplesQueried.length; i++) {
for (let j = 0; j < categories.length; j++) {
let cat = categories[j]
if (!(cat in categoryCounts))
categoryCounts[cat] = {}
let val = sampleResults[i][j]
if (!(val in categoryCounts[cat]))
categoryCounts[cat][val] = 0
categoryCounts[cat][val] += 1
}
}
for (let j = 0; j < categories.length; j++){
let cat = categories[j]
let sum = 0
let maxval = -1
let maxkey = null
for (let key in categoryCounts[cat]) {
let val = categoryCounts[cat][key]
sum += val
if (key !== "Not provided" && val > maxval) {
maxval = val
maxkey = key
}
}
let me = samplesQueried.indexOf(state.barcode_prefix + state.sample_id);
let my_cat = categories.indexOf(cat);
let my_value = sampleResults[me][my_cat];
let set_color = null;
let chosen = null
if (!(cat in chooserMap) || chooserMap[cat]["type"] === "max") {
chosen = maxkey
if(chosen === my_value) {
set_color = 'similarity-fontstyle-same';
} else {
set_color = 'similarity-fontstyle-different';
}
}
else if (chooserMap[cat]["type"] === "specified")
chosen = chooserMap[cat]["value"]
else if (chooserMap[cat]["type"] === "same") {
me = samplesQueried.indexOf(state.barcode_prefix + state.sample_id)
j = categories.indexOf(cat)
chosen = sampleResults[me][j]
}
display[cat] = {}
if(chosen in dynamic_text_dictionary) {
display[cat]["response"] = dynamic_text_dictionary[chosen];
} else {
display[cat]["response"] = chosen;
}
display[cat]["value"] = Math.round((categoryCounts[cat][chosen] / sum) * 100) + "%"
display[cat]["color"] = set_color;
}
for (let cat of categories) {
if (!(cat in selectorMap))
continue;
let resp_selector = selectorMap[cat][0]
let val_selector = selectorMap[cat][1]
let resp = display[cat]["response"]
let val = display[cat]["value"]
let color = display[cat]["color"]
$(val_selector).text(val).removeClass("spinner-grow spinner-grow-sm");
if(color !== null) {
$(resp_selector).text(resp).removeClass("spinner-grow spinner-grow-sm text-success").addClass(color);
} else {
$(resp_selector).text(resp).removeClass("spinner-grow spinner-grow-sm");
}
}
}
}
function queryNeighborAndSelfMetadata(state, metadata_cats){
return function(result, textStatus, jqXHR)
{
let toQuery = result;
toQuery.push(state.barcode_prefix + state.sample_id);
return $.ajax(
{
method: "POST",
url: state.public_endpoint + '/dataset/' + state.dataset_input.value + "/metadata/values?" + $.param({ cat: metadata_cats }, true), // The true indicates traditional mode, which produces cat=blah&cat=blah rather than cat[]=blah&cat[]=blah which crashes the server.
data: JSON.stringify(toQuery),
contentType: "application/json"
}).fail(function(result, textStatus, errorThrown){
console.log("Couldn't retrieve metadata for neighbors and self " + errorThrown)
}).then(function(result, textStatus, jqXHR){
let thenner = {};
thenner.then = function(func){
// Need to pass on the sample ids. Argh.
return func(toQuery, result);
};
return thenner;
});
};
}
function updateCompare(state){
// Reset all the fields to spinners
$(".info-loader").empty().addClass("spinner-grow spinner-grow-sm");
// Stuff to fill in:
// sample_type, n_bacteria, n_archaea, dataset_name,
// n_bacteria_background, n_archaea_background,
// age_nearest_neighbor, more_or_less_sweets_nearest_neighbor
function retrieveText(method, url, data){
return $.ajax({
method: method,
url: url,
data: JSON.stringify(data),
contentType: "application/json"
}).fail(function(result, textStatus, errorThrown){
console.log("Couldn't retrieve text for " + method + " " + url);
});
}
function setInfoText(resultSelector){
return function(result, textStatus, jqXHR){
return $(resultSelector).text(result).removeClass("spinner-grow spinner-grow-sm");
};
}
function fillResults(state, selectors)
{
return function(samplesQueried, sampleResults)
{
// First selector, age, Second selector, sweets
// No similarity between the two, so we just have to handle both
let me = samplesQueried.pop();
let my_data = sampleResults.pop();
if (me !== (state.barcode_prefix + state.sample_id))
console.log("Bad call to fill results, sample id mismatch");
for (let selector_index = 0; selector_index < selectors.length; selector_index++)
{
if (selectors[selector_index] === "#age_nearest_neighbor")
{
// Find age of first neighbor with age
let nearest_age = "{{ _('Unspecified') }}";
for (let i = 0; i < samplesQueried.length; i++)
{
if (sampleResults[i][selector_index] !== "{{ _('Unspecified') }}")
{
nearest_age = Math.round(sampleResults[i][selector_index]);
break;
}
}
if (nearest_age === "{{ _('Unspecified') }}")
setInfoText(selectors[selector_index])("{{ _('chose not to provide their age') }}", null, null);
else
setInfoText(selectors[selector_index])("{{ _('is') }} " + nearest_age + " {{ _('years old') }}", null, null);
}
if (selectors[selector_index] === "#more_or_less_sweets_nearest_neighbor")
{
// Find string value for first neighbor with a string value
let nearest_sweets = "{{ _('Unspecified') }}";
for (let i = 0; i < samplesQueried.length; i++)
{
if (sampleResults[i][selector_index] !== "{{ _('Unspecified') }}" &&
sampleResults[i][selector_index] !== "{{ _('Not provided') }}")
{
nearest_sweets = sampleResults[i][selector_index];
break;
}
}
// Comparing metadata is an absolute nightmare.
let possible_values = {
"{{ _('Unspecified') }}" : NaN,
"{{ _('Not provided') }}" : NaN,
"{{ _('Never') }}" : 0,
"{{ _('Rarely (less than once/week)') }}" : 1,
"{{ _('Occasionally (1-2 times/week)') }}" : 2,
"{{ _('Regularly (3-5 times/week)') }}" : 3,
"{{ _('Daily') }}": 4
}
let my_sweets = possible_values[my_data[selector_index]];
let their_sweets = possible_values[nearest_sweets];
let info_text = "";
if (isNaN(my_sweets)){
if (isNaN(their_sweets))
info_text = "{{ _('chose not to say how many sweets they eat') }}";
else
info_text = nearest_sweets.toLowerCase() + " {{ _('eats sweets') }}";
}
else{
if (my_sweets < their_sweets)
info_text = "{{ _('eats more sugary sweets than you') }}";
else if (my_sweets > their_sweets)
info_text = "{{ _('eats fewer sugary sweets than you') }}";
else if (my_sweets === their_sweets)
info_text = "{{ _('eats about the same number of sugary sweets as you') }}";
else
info_text = "{{ _('chose not to say how many sweets they eat') }}";
}
setInfoText(selectors[selector_index])(info_text, null, null);
}
}
}
}
$("#sample_type").text(state.sample_type).removeClass("spinner-grow spinner-grow-sm");
$("#dataset_name").text(state.dataset_input.value).removeClass("spinner-grow spinner-grow-sm");
// TODO: Fill in these URLs
retrieveText("GET", state.public_endpoint + "/dataset/" + state.dataset_input.value + "/taxonomy/single/" + state.taxonomy + "/" + state.barcode_prefix + state.sample_id + "/counts?level=Kingdom", null).then(
function(result, textStatus, jqXHR){
$("#n_bacteria").text(result["Bacteria"].toLocaleString()).addClass("microbe-count").removeClass("spinner-grow spinner-grow-sm");
$("#n_archaea").text(result["Archaea"].toLocaleString()).addClass("microbe-count").removeClass("spinner-grow spinner-grow-sm");
});
retrieveText(
"POST",
state.public_endpoint + "/dataset/" + state.dataset_input.value + "/taxonomy/group/" + state.taxonomy + "/counts?level=Kingdom",
{"sample_ids":[]}
).then(
function(result, textStatus, jqXHR){
$("#n_bacteria_background").text(result["Bacteria"].toLocaleString()).addClass("microbe-count").removeClass("spinner-grow spinner-grow-sm");
$("#n_archaea_background").text(result["Archaea"].toLocaleString()).addClass("microbe-count").removeClass("spinner-grow spinner-grow-sm");
});
retrieveNeighbors(state, 1)
.then(queryNeighborAndSelfMetadata(state, ["age_cat", "sugary_sweets_frequency"]))
.then(fillResults(state, ["#age_nearest_neighbor", "#more_or_less_sweets_nearest_neighbor"]));
}
function updateDiversity(state){
//https://www-dev.ucsd.edu/results-api/diversity/alpha/group/faith_pd?summary_statistics=true
const more_than_30_plants =
{
"metadata_query":
{
"condition": "OR",
"rules": [
{
"id": "types_of_plants",
"operator": "equal",
"value": "More than 30"
}
]
}
};
const water_frequency =
{
"metadata_query":
{
"condition": "OR",
"rules": [
{
"id": "one_liter_of_water_a_day_frequency",
"operator": "equal",
"value": "Regularly (3-5 times/week)"
}
]
}
};
const exercise_regularly =
{
"metadata_query":
{
"condition": "OR",
"rules": [
{
"id": "exercise_frequency",
"operator": "equal",
"value": "Regularly (3-5 times/week)"
}
]
}
};
//I wish we had ordered categorical variables because this query is stupid
const sleep_more_than_6_hrs =
{
"metadata_query":
{
"condition": "OR",
"rules": [
{
"id": "sleep_duration",
"operator": "equal",
"value": "6-7 hours"
},
{
"id": "sleep_duration",
"operator": "equal",
"value": "7-8 hours"
},