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Commit aff6d813 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add holders for all data

parent 92b4238d
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3 merge requests!9Develop,!7Develop,!6Add.multiple.data
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archetypes/sc_data.md 0 → 100644
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---
title: "{{ replace .Name "-" " " | title }}"
description: "Single-Cell RNA-sequencing Data"
name: "(PENDING)"
date: {{ .Date }}
draft: true
weight: ""
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
config.toml
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− 2
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......@@ -59,8 +59,8 @@ paginate = 10
name = "Single-Cell Data"
pre = "<i class='fas fa-chart-bar fa-fw'></i>"
weight = 5
identifier = "data"
url = "/data"
identifier = "sc.data"
url = "/sc.data/"
[[menu.main]]
name = "Contact"
pre = "<i class='fas fa-phone fa-fw'></i>"
......
content/data.md deleted 100644 → 0
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---
title: "Single-Cell RNA-seq Data"
date: 2019-06-10T21:49:01-05:00
draft: false
type: "custom"
layout: "data"
---
content/sc.data/_index.md 0 → 100644
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---
title: "Single-Cell RNA-sequencing Data"
date: 2019-05-19T12:09:34-05:00
draft: true
type: "custom"
layout: "sc.data"
---
content/sc.data/hu.bph.pr.md 0 → 100644
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---
title: "Human BPH"
description: "Single-Cell RNA-sequencing Data"
name: "Human BPH (PENDING)"
date: 2019-12-24T22:35:01-06:00
draft: true
weight: "4"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
content/sc.data/hu.cancer.pr.md 0 → 100644
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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: true
weight: "5"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
content/sc.data/hu.donor.bl.md 0 → 100644
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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: true
weight: "3"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
content/sc.data/hu.donor.pr.deep.md 0 → 100644
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---
title: "Human Donor Prostate (deep)"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor (additional sequencing depth of data published in Henry GH. et al, Cell Reports,2018)"
date: 2019-12-24T21:46:39-06:00
draft: true
weight: "1"
type: "custom"
layout: "hu.donor.deep"
---
content/sc.data/hu.donor.pr.shallow.md 0 → 100644
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---
title: "Human Donor Prostate (shallow)"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor (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"
---
content/sc.data/mu.bl.md 0 → 100644
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− 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: true
weight: "7"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
content/sc.data/mu.pr.md 0 → 100644
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− 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: true
weight: "6"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
data/sc_data/hu_donor_shallow/genes.json 0 → 100644
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This source diff could not be displayed because it is too large. You can view the blob instead.
layouts/custom/hu.donor.deep.html 0 → 100644
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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: 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>
<body>
<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 data is the
result of additional sequencing done on the same samples post publication.
</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 class="img">
<img id="img.ClusterVis" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.Feature">
</h3>
<div class="img">
<img id="img.Feature" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.ViolinBox">
</h3>
<div 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>
</body>
{{ 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_deep.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_deep.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.deep/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/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/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
</head>
\ No newline at end of file
layouts/custom/data.html → layouts/custom/hu.donor.shallow.html
+ 191
− 0
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......@@ -9,10 +9,11 @@
</div>
<style>
.content{
.content {
margin: 0;
max-width: none;
}
.select {
float: top;
z-index: 1;
......@@ -21,38 +22,46 @@
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{
img {
max-width: 100%;
height: auto;
}
@media (max-width: 1000px) {
.columnS {
text-align: right;
width: 100%;
}
.columnF {
width: 100%;
}
br {
display: none;
}
}
</style>
<body>
<div class="select">
<div class="columnS ui-widget">
......@@ -63,7 +72,7 @@
<div class="columnS">
<label for="populations" style="font-size:18px;">
<b>Select a group of cell populations:</b>
</label>
</label>
<br>
<select name="populations" id="populations">
<option selected="selected" value="Population"> Cell Populations</option>
......@@ -80,12 +89,12 @@
<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.
<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>
......@@ -93,93 +102,90 @@
<h1 id="label.gene">NO GENE SELECTED</h1>
<h2 id="label.populations"></h2>
<div class="columnF">
<h4 id="label.ClusterVis"></h3>
<div class="img">
<img id="img.ClusterVis" src="" />
</div>
<br>
<h4 id="label.ClusterVis">
</h3>
<div class="img">
<img id="img.ClusterVis" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.Feature"></h3>
<div class="img">
<img id="img.Feature" src="" />
</div>
<br>
<h4 id="label.Feature">
</h3>
<div class="img">
<img id="img.Feature" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.ViolinBox"></h3>
<div class="img">
<img id="img.ViolinBox" src="" />
</div>
<br>
<h4 id="label.ViolinBox">
</h3>
<div 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"
<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"
<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><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
W-R8CM</a></span></div>
</div>
</body>
{{ 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>
<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>
.ui-autocomplete {
max-height: 200px;
overflow-y: auto;
overflow-x: hidden;
}
</style>
<script>
$(function(){
$("#populations" ).selectmenu({width: 230});
});
$(function(){
var genes = {{ index .Site.Data.scRNAseq_huPr_D.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.scRNAseq_huPr_D.genes }};
_gene = $("#gene").val().toUpperCase();
if($.inArray(_gene,genes.genes) < 0){
alert("Gene "+ _gene +" not exist in the data.")
return
}
<!-- alert(_gene) -->
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.deep/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/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/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return(_gene)
});
</script>
$(function () {
$("#populations").selectmenu({ width: 230 });
});
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_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_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.shallow/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.shallow/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.shallow/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
</head>
\ No newline at end of file
layouts/custom/repository.html → layouts/custom/sc.data.html
+ 14
− 0
View file @ aff6d813
{{ partial "header.html" . }}
<div class="header">
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
</div>
<div class="content">
{{ .Content }}
{{ range .Pages.ByWeight }}
<li><a href="{{.Permalink}}">{{.Params.name}}</a></li>
{{ end }}
</div>
{{ partial "footer.html" . }}
\ No newline at end of file
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