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Commit 906d0ebb authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge branch 'add.muPrUr' into 'develop' 

Add.mu pr ur

See merge request !31
parents 1564eeee b134d9a2
2 merge requests!32Develop,!31Add.mu pr ur
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---
title: "{{ replace .Name "-" " " | title }}"
description: "Single-Cell RNA-sequencing Data"
name: "(PENDING)"
date: {{ .Date }}
draft: true
weight: ""
type: "custom"
layout: ""
current: true
---
---
title: "{{ replace .Name "-" " " | title }}"
description: "Single-Cell RNA-sequencing Data"
name: "(PENDING)"
date: {{ .Date }}
draft: true
weight: ""
type: "custom"
layout: ""
current: true
---
**PENDING**
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---
title: "Human Donor Prostate"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor Prostate (additional sequencing depth of data published in Henry GH. et al, Cell Reports,2018 and projected in UMAP space)"
name: "Human Donor Prostate"
date: 2019-12-24T21:46:39-06:00
draft: false
weight: "1"
type: "custom"
layout: "hu.donor.deep"
layout: "hu.Pd.deep"
current: true
aliases: /analysis.php
---
......
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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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---
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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---
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
---
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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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---
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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---
title: "Human Donor Bladder"
title: "Mouse Prostate and Urethra"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor Bladder (PENDING)"
date: 2019-12-24T22:35:48-06:00
draft: false
name: "Mouse Prostate and Urethra"
date: 2020-02-19T23:28:10-06:00
draft: true
weight: "3"
type: "custom"
layout: ""
current: false
layout: "muPrUr"
current: true
---
**PENDING**
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......@@ -77,8 +77,7 @@
<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>
<option value="Region">Prostatic Region</option>
</select>
</div>
<div class="columnS">
......@@ -88,8 +87,8 @@
<br>
<select name="group" id="group">
<option selected="selected" value="all">All Cells</option>
<option value="epi">Epithelia Only</option>
<option value="st">Stroma Only</option>
<option value="dis">Distal Prostate</option>
<option value="prx">Proximal Prostate</option>
</select>
</div>
<br>
......@@ -173,7 +172,7 @@
$("#group").selectmenu({ width: 220 });
});
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
var genes = {{ index .Site.Data.sc_data.hu.genes }};
var selectedGene = $("#gene").autocomplete({
source: genes.genes,
maxResults: 10,
......@@ -183,7 +182,7 @@
});
$("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
var genes = {{ index .Site.Data.sc_data.hu.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
if (_gene == "") {
......@@ -198,13 +197,13 @@
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-2.amazonaws.com/data.images.gse117403.deep/" + $("#group").val() + "/images/" + $("#populations").val() + "/umap.png"
img.src = "https://s3.us-east-1.amazonaws.com/data.images.pd.deep/" + $("#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-2.amazonaws.com/data.images.gse117403.deep/" + $("#group").val() + "/images/umap/" + "genes/" + _gene + "_1.png"
img.src = "https://s3.us-east-1.amazonaws.com/data.images.pd.deep/" + $("#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-2.amazonaws.com/data.images.gse117403.deep/" + $("#group").val() + "/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
img.src = "https://s3.us-east-1.amazonaws.com/data.images.pd.deep/" + $("#group").val() + "/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
......
layouts/custom/hu.donor.shallow.html → layouts/custom/muPrUr.html
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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>
{{ 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>Tissue</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="pr">Prostate Only</option>
<option value="ur">Urethra Only</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 C57BL/6 mouse prostates and urethra. 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, or tissue source.
</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">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>
</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.mu.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.mu.genes }};
_gene = $("#gene").val().charAt(0).toUpperCase() + $("#gene").val().slice(1).toLowerCase();
if ($.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.muprur/" + $("#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.muprur/" + $("#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.muprur/" + $("#group").val() + "/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
</head>
\ No newline at end of file
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