diff --git a/content/sc.data/PdPgb.md b/content/sc.data/PdPgb.md new file mode 100644 index 0000000000000000000000000000000000000000..5d3d398a6fd1579096a19ce4de4190ac9ba23926 --- /dev/null +++ b/content/sc.data/PdPgb.md @@ -0,0 +1,11 @@ +--- +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 +--- diff --git a/content/sc.data/muPrUr.md b/content/sc.data/muPrUr.md index 7e8c2ba871f42b1ebb80d084e3a970806487c994..efd89387b6c15dd823a1fb6dbc87b87182eb0f1b 100644 --- a/content/sc.data/muPrUr.md +++ b/content/sc.data/muPrUr.md @@ -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 --- diff --git a/layouts/custom/hu.PdPgb.html b/layouts/custom/hu.PdPgb.html new file mode 100644 index 0000000000000000000000000000000000000000..db6bb5c72f497bcd3f1ed3aaa0cea113c1e81c91 --- /dev/null +++ b/layouts/custom/hu.PdPgb.html @@ -0,0 +1,216 @@ +{{ 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 diff --git a/layouts/custom/muPrUr.html b/layouts/custom/mu.PrUr.html similarity index 93% rename from layouts/custom/muPrUr.html rename to layouts/custom/mu.PrUr.html index 26395cffaaba0420c977d86cea9af5023a521fba..64807222ad4cb7a7580d9398bf71c78b0b835d99 100644 --- a/layouts/custom/muPrUr.html +++ b/layouts/custom/mu.PrUr.html @@ -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>