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Commit 7ed4073c authored by Gervaise Henry's avatar Gervaise Henry
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Remove pending sc data pages

parent 1564eeee
2 merge requests!32Develop,!31Add.mu pr ur
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archetypes/sc_data.md → archetypes/sc.data.md
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--- ---
title: "{{ replace .Name "-" " " | title }}" title: "{{ replace .Name "-" " " | title }}"
description: "Single-Cell RNA-sequencing Data" description: "Single-Cell RNA-sequencing Data"
name: "(PENDING)" name: "(PENDING)"
date: {{ .Date }} date: {{ .Date }}
draft: true draft: true
weight: "" weight: ""
type: "custom" type: "custom"
layout: "" layout: ""
current: true current: true
--- ---
**PENDING** **PENDING**
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content/sc.data/hu.bph.pr.md deleted 100644 → 0
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---
title: "Human BPH"
description: "Single-Cell RNA-sequencing Data"
name: "Human BPH Prostate (PENDING)"
date: 2019-12-24T22:35:01-06:00
draft: false
weight: "4"
type: "custom"
layout: ""
current: false
---
**PENDING**
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content/sc.data/hu.cancer.pr.md deleted 100644 → 0
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---
title: "Human Prostate Cancer"
description: "Single-Cell RNA-sequencing Data"
name: "Human Prostate Cancer (PENDING)"
date: 2019-12-24T22:35:22-06:00
draft: false
weight: "5"
type: "custom"
layout: ""
current: false
---
**PENDING**
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content/sc.data/hu.donor.bl.md deleted 100644 → 0
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---
title: "Human Donor Bladder"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor Bladder (PENDING)"
date: 2019-12-24T22:35:48-06:00
draft: false
weight: "3"
type: "custom"
layout: ""
current: false
---
**PENDING**
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content/sc.data/hu.donor.pr.shallow.md deleted 100644 → 0
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---
title: "Human Donor Prostate (shallow)"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor Prostate (original sequencing depth published in Henry GH. et al, Cell Reports,2018)"
date: 2019-12-24T21:46:39-06:00
draft: true
weight: "2"
type: "custom"
layout: "hu.donor.shallow"
current: false
---
content/sc.data/mu.bl.md deleted 100644 → 0
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---
title: "Mouse Bladder"
description: "Single-Cell RNA-sequencing Data"
name: "Mouse Bladder (PENDING)"
date: 2019-12-24T22:36:05-06:00
draft: false
weight: "7"
type: "custom"
layout: ""
current: false
---
**PENDING**
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content/sc.data/mu.pr.md deleted 100644 → 0
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---
title: "Mouse Prostate"
description: "Single-Cell RNA-sequencing Data"
name: "Mouse Prostate (PENDING)"
date: 2019-12-24T22:36:01-06:00
draft: false
weight: "6"
type: "custom"
layout: ""
current: false
---
**PENDING**
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data/sc_data/hu_donor_pr_shallow/genes.json deleted 100644 → 0
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layouts/custom/hu.donor.shallow.html deleted 100644 → 0
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{{ partial "header.html" . }}
<div class="header">
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
</div>
<style>
.content {
margin: 0;
max-width: none;
}
.select {
float: top;
z-index: 1;
top: 0px;
background: #191818;
overflow-x: hidden;
padding: 8px 10px;
}
.columnS {
float: left;
text-align: center;
width: 50%;
}
.columnF {
float: left;
text-align: center;
width: 33.33%;
}
.row:after {
content: "";
display: table;
clear: both;
}
img {
max-width: 100%;
height: auto;
}
@media (max-width: 1000px) {
.columnS {
text-align: right;
width: 100%;
}
.columnF {
width: 100%;
}
br {
display: none;
}
}
</style>
<div class="content">
<div class="select">
<div class="columnS ui-widget">
<label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
<br>
<input id="gene" size="19">
</div>
<div class="columnS">
<label for="populations" style="font-size:18px;">
<b>Select a group of cell populations:</b>
</label>
<br>
<select name="populations" id="populations">
<option selected="selected" value="Population"> Cell Populations</option>
<option>Lineage</option>
<option value="Zone">Prostatic Zone</option>
<option>Patient</option>
</select>
</div>
<br>
<div style="text-align:center">
<button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
</div>
<hr>
<div>
<span style="font-size:16px; font-weight:bold;">Experimental details:</span>
<br>
<span style="font-size:16px;">
Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from
the prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were
clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can
be compared by population identity, cell lineage, patient, or dissected prostatic zone. This is the
original sequencing depth published.
</span>
</div>
</div>
<div align="center">
<h1 id="label.gene">NO GENE SELECTED</h1>
<h2 id="label.populations"></h2>
<div class="columnF">
<h4 id="label.ClusterVis">
</h3>
<div data-proofer-ignore class="img">
<img id="img.ClusterVis" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.Feature">
</h3>
<div data-proofer-ignore class="img">
<img id="img.Feature" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.ViolinBox">
</h3>
<div data-proofer-ignore class="img">
<img id="img.ViolinBox" src="" />
</div>
<br>
</div>
</div>
<hr>
<div align="left">
<div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
<div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
target="_blank">Cell Reports</a></span></div>
<div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
<div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
target="_blank">GEO:
GSE117403</a></span></div>
<div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
W-R8CM</a></span></div>
</div>
</div>
{{ partial "footer.html" . }}
<head>
<link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
<style>
.ui-autocomplete {
max-height: 200px;
overflow-y: auto;
overflow-x: hidden;
}
</style>
<script>
$(function () {
$("#populations").selectmenu({ width: 230 });
});
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
var selectedGene = $("#gene").autocomplete({
source: genes.genes,
maxResults: 10,
maxShowItems: 10,
minLength: 1,
});
});
$("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
alert("Gene " + _gene + " not exist in the data.")
return
}
document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
var img = document.getElementById("img.ClusterVis");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
document.getElementById("label.Feature").innerHTML = "Feature Plot"
var img = document.getElementById("img.Feature");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/tsne/" + "genes/" + _gene + "_1.png"
document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
var img = document.getElementById("img.ViolinBox");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
</head>
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