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Commit 60ffbdfc authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge branch '3-add.PdPgb' into 'develop' 

Resolve "Add PdPgb data"

Closes #3

See merge request !35
parents d10f3736 faa1bd3f
2 merge requests!36Develop,!35Resolve "Add PdPgb data"
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content/sc.data/PdPgb.md 0 → 100644
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---
title: "Human Normal and BPH Prostate"
description: "Single-Cell RNA-sequencing Data"
name: "Human Normal and BPH Prostate"
date: 2020-02-22T20:10:33-06:00
draft: false
weight: "2"
type: "custom"
layout: "hu.PdPgb"
current: true
---
content/sc.data/muPrUr.md
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......@@ -6,6 +6,6 @@ date: 2020-02-19T23:28:10-06:00
draft: false
weight: "3"
type: "custom"
layout: "muPrUr"
layout: "mu.PrUr"
current: true
---
layouts/custom/hu.PdPgb.html 0 → 100644
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− 0
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{{ partial "header.html" . }}
<div class="header">
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
</div>
<div class="content">
{{ .Content }}
</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: 33.33%;
}
.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: 1250px) {
.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="Region">Prostatic Region</option>
<option>Phenotype</option>
</select>
</div>
<div class="columnS">
<label for="group" style="font-size:18px;">
<b>Select a group of cell to display:</b>
</label>
<br>
<select name="group" id="group">
<option selected="selected" value="all">All Cells</option>
<option value="dis">Distal Prostate</option>
<option value="prx">Proximal Prostate</option>
<option value="nor">Normal Prostate</option>
<option value="bph">BPH Prostate</option>
</select>
</div>
<br>
<div style="text-align:left">
<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 data is the
result of additional sequencing done on the same samples post publication, and projected in UMAP space.
</span>
</div>
</div>
<div align="center">
<h1 id="label.gene">NO GENE SELECTED</h1>
<h2 id="label.populations"></h2>
<h3 id="label.group"></h3>
<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://doi.org/10.1101/2020.02.19.937615"
target="_blank">bioRxiv</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://doi.org/10.1101/2020.02.19.937615"
target="_blank">Human Normal Prostate GEO: GSEXXX</a></span></div>
<div><span style="font-size:16px;"> <a href="https://doi.org/10.1101/2020.02.19.937615"
target="_blank">Human Glandular BPH Prostate GEO: GSEXXX</a></span></div>
<div><span style="font-size:16px;"><a href="https://www.gudmap.org/chaise/record/#2/RNASeq:Study/RID=16-WPBT" target="_blank">Normal Human Prostate GUDMAP:
16-WPBT</a></span></div>
<div><span style="font-size:16px;"><a href="https://www.gudmap.org/chaise/record/#2/RNASeq:Study/RID=16-WPBW" target="_blank">Glandular BPH Human Prostate GUDMAP:
16-WPBW</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: 220, height: 1 });
});
$(function () {
$("#group").selectmenu({ width: 220 });
});
$(function () {
var genes = {{ index .Site.Data.sc_data.hu.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.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
if (_gene == "") {
alert("No Gene Selected.")
} else {
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.group").innerHTML = $("#group").val().toUpperCase() + " CELLS"
document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
var img = document.getElementById("img.ClusterVis");
img.src = "https://s3.us-east-1.amazonaws.com/data.images.pdpgb/" + $("#group").val() + "/images/" + $("#populations").val() + "/umap.png"
document.getElementById("label.Feature").innerHTML = "Feature Plot"
var img = document.getElementById("img.Feature");
img.src = "https://s3.us-east-1.amazonaws.com/data.images.pdpgb/" + $("#group").val() + "/images/umap/" + "genes/" + _gene + "_1.png"
document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
var img = document.getElementById("img.ViolinBox");
img.src = "https://s3.us-east-1.amazonaws.com/data.images.pdpgb/" + $("#group").val() + "/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
</head>
\ No newline at end of file
layouts/custom/muPrUr.html → layouts/custom/mu.PrUr.html
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......@@ -145,8 +145,10 @@
target="_blank">Mouse Prostate GEO: GSEXXX</a></span></div>
<div><span style="font-size:16px;"> <a href="https://doi.org/10.1101/2020.02.19.937615"
target="_blank">Mouse Urethra GEO: GSEXXX</a></span></div>
<div><span style="font-size:16px;"><a href="https://doi.org/10.25548/16-WM8C" target="_blank">GUDMAP:
16-WM8C</a></span></div>
<div><span style="font-size:16px;"><a href="https://www.gudmap.org/chaise/record/#2/RNASeq:Study/RID=16-WPC0" target="_blank">Normal Human Prostate GUDMAP:
16-WPC0</a></span></div>
<div><span style="font-size:16px;"><a href="https://www.gudmap.org/chaise/record/#2/RNASeq:Study/RID=16-WPC2" target="_blank">Glandular BPH Human Prostate GUDMAP:
16-WPC2</a></span></div>
</div>
</div>
......
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