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Commit 4e70e75e authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Data update 

Remove Biorepository temporarily
Remove rss feeds
Remove Epi/St only option
Move data to deep sequencing hosted on BICF bicket
parent 4ad34110
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3 merge requests!9Develop,!7Develop,!5Data update
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config.toml
+ 6
− 6
View file @ 4e70e75e
...@@ -49,12 +49,12 @@ paginate = 10 ...@@ -49,12 +49,12 @@ paginate = 10
weight = 3 weight = 3
identifier = "publications" identifier = "publications"
url = "/publications/" url = "/publications/"
[[menu.main]] # [[menu.main]]
name = "Biorepository" # name = "Biorepository"
pre = "<i class='fas fa-stethoscope fa-fw'></i>" # pre = "<i class='fas fa-stethoscope fa-fw'></i>"
weight = 4 # weight = 4
identifier = "repository" # identifier = "repository"
url = "/repository/" # url = "/repository/"
[[menu.main]] [[menu.main]]
name = "Single-Cell Data" name = "Single-Cell Data"
pre = "<i class='fas fa-chart-bar fa-fw'></i>" pre = "<i class='fas fa-chart-bar fa-fw'></i>"
......
data/scRNAseq_huPr_D/genes.json
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− 4
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layouts/custom/data.html
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− 29
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...@@ -24,7 +24,7 @@ ...@@ -24,7 +24,7 @@
.columnS { .columnS {
float: left; float: left;
text-align: center; text-align: center;
width: 33.33%; width: 50%;
} }
.columnF { .columnF {
float: left; float: left;
...@@ -61,28 +61,21 @@ ...@@ -61,28 +61,21 @@
<input id="gene" size="19"> <input id="gene" size="19">
</div> </div>
<div class="columnS"> <div class="columnS">
<label for="lineage" style="font-size:18px;"><b>Select a cell lineage to <label for="populations" style="font-size:18px;">
display:</b></label> <b>Select a group of cell populations:</b>
<br> </label>
<select name="lineage" id="lineage">
<option selected="selected" value="all">All Cells</option>
<option value="epi">Epithelial Cells Only</option>
<option value="st">Stromal Cells Only</option>
</select>
</div>
<div class="columnS">
<label for="populations" style="font-size:18px;"><b>Select a group of cell
populations:</b></label>
<br> <br>
<select name="populations" id="populations"> <select name="populations" id="populations">
<option selected="selected" value="Population"> Cell Populations</option>
<option>Lineage</option> <option>Lineage</option>
<option>Patient</option>
<option selected="selected" value="Populations"> Cell Populations</option>
<option value="Zone">Prostatic Zone</option> <option value="Zone">Prostatic Zone</option>
<option>Patient</option>
</select> </select>
</div> </div>
<br> <br>
<button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button> <div style="text-align:center">
<button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
</div>
<hr> <hr>
<div> <div>
<span style="font-size:16px; font-weight:bold;">Experimental details:</span> <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
...@@ -92,13 +85,13 @@ ...@@ -92,13 +85,13 @@
of three 18-38 year old organ donors using the 10x Genomics platform. of three 18-38 year old organ donors using the 10x Genomics platform.
The cells were clustered and identified by correlation of their The cells were clustered and identified by correlation of their
transcriptomes to known cell types. Gene expression can be compared by transcriptomes to known cell types. Gene expression can be compared by
population identity, cell lineage, patient, or dissected prostatic zone.</span> population identity, cell lineage, patient, or dissected prostatic zone.
</span>
</div> </div>
</div> </div>
<div align="center"> <div align="center">
<h1 id="label.gene">NO GENE SELECTED</h1> <h1 id="label.gene">NO GENE SELECTED</h1>
<h2 id="label.lineage"></h2> <h2 id="label.populations"></h2>
<h3 id="label.populations"></h3>
<div class="columnF"> <div class="columnF">
<h4 id="label.ClusterVis"></h3> <h4 id="label.ClusterVis"></h3>
<div class="img"> <div class="img">
...@@ -137,6 +130,7 @@ ...@@ -137,6 +130,7 @@
</div> </div>
</body> </body>
{{ partial "footer.html" . }}
<head> <head>
<link rel="stylesheet" <link rel="stylesheet"
...@@ -153,9 +147,6 @@ ...@@ -153,9 +147,6 @@
} }
</style> </style>
<script> <script>
$(function(){
$("#lineage" ).selectmenu({width: 230});
});
$(function(){ $(function(){
$("#populations" ).selectmenu({width: 230}); $("#populations" ).selectmenu({width: 230});
}); });
...@@ -178,20 +169,17 @@ ...@@ -178,20 +169,17 @@
} }
<!-- alert(_gene) --> <!-- alert(_gene) -->
document.getElementById("label.gene").innerHTML = _gene document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.lineage").innerHTML = $("#lineage").val().toUpperCase() + " Cells"
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase() document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization" document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
var img = document.getElementById("img.ClusterVis"); var img = document.getElementById("img.ClusterVis");
img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/ID/" + $("#lineage").val() + "/" + $("#populations").val() + "/ClusterVis.png" 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" document.getElementById("label.Feature").innerHTML = "Feature Plot"
var img = document.getElementById("img.Feature"); var img = document.getElementById("img.Feature");
img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/Feature/" + $("#lineage").val() + "/genes/" + _gene + ".png" 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" document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
var img = document.getElementById("img.ViolinBox"); var img = document.getElementById("img.ViolinBox");
img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/ViolinBox/" + $("#lineage").val() + "/" + $("#populations").val() + "/" + _gene + ".png" img.src="https://s3.us-east-2.amazonaws.com/data.images.gse117403.deep/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return(_gene) return(_gene)
}); });
</script> </script>
</head> </head>
\ No newline at end of file
{{ partial "footer.html" . }}
\ No newline at end of file
layouts/partials/social.html
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<div class="pure-menu social"> <div class="pure-menu social">
<ul class="pure-menu-list"> <ul class="pure-menu-list">
{{ if .OutputFormats.Get "RSS" }}
<li class="pure-menu-item">
<a class="pure-menu-link" href='{{ with .OutputFormats.Get "RSS" }}{{ .RelPermalink }}{{ end }}'><i
class="fas fa-rss"></i>RSS</a>
</li>
{{ end }}
<!-- SNS microblogging --> <!-- SNS microblogging -->
{{ with .Site.Social.twitter }} {{ with .Site.Social.twitter }}
......
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