Merge branch 'repository' into 'develop'

Repository

See merge request !8

config.toml

@@ -49,12 +49,12 @@ paginate = 10
     weight = 3
     identifier = "publications"
     url = "/publications/"
-#  [[menu.main]]
-#    name = "Biorepository"
-#    pre = "<i class='fas fa-stethoscope fa-fw'></i>"
-#    weight = 4
-#    identifier = "repository"
-#    url = "/repository/"
+  [[menu.main]]
+    name = "Biorepository"
+    pre = "<i class='fas fa-stethoscope fa-fw'></i>"
+    weight = 4
+    identifier = "repository"
+    url = "/repository/"
   [[menu.main]]
     name = "Single-Cell Data"
     pre = "<i class='fas fa-chart-bar fa-fw'></i>"

data/repository/filters.json

+[
+    {"id": "disease", "parent": "#", "text": "Disease Phenotype",  "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "disease.d", "parent":"disease", "text": "Donor (normal)"},
+    {"id": "disease.b", "parent":"disease", "text": "BPH"},
+    {"id": "disease.c", "parent":"disease", "text": "Prostate Cancer"},
+    {"id": "demographics", "parent": "#", "text": "Demographics",  "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "ethnicity", "parent":"demographics", "text": "Ethnicity", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "ethn.aa", "parent":"ethnicity", "text": "African American"},
+    {"id": "ethn.as", "parent":"ethnicity", "text": "Asian"},
+    {"id": "ethn.ca", "parent":"ethnicity", "text": "Caucasian"},
+    {"id": "ethn.hi", "parent":"ethnicity", "text": "Hispanic"},
+    {"id": "ethn.uk", "parent":"ethnicity", "text": "Unknown Ethnicity"},
+    {"id": "age", "parent":"demographics", "text": "Age", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "age.40", "parent":"age", "text": "<40yo"},
+    {"id": "age.50", "parent":"age", "text": "41-50yo"},
+    {"id": "age.60", "parent":"age", "text": "51-60yo"},
+    {"id": "age.70", "parent":"age", "text": "61-70yo"},
+    {"id": "age.80", "parent":"age", "text": "71-80yo"},
+    {"id": "age.90", "parent":"age", "text": "81-90yo"},
+    {"id": "age.100", "parent":"age", "text": "91+yo"},
+    {"id": "age.uk", "parent":"age", "text": "Unknown Age"},
+    {"id": "clinical", "parent":"#", "text": "Clinical Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bmi", "parent":"clinical", "text": "BMI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bmi.uw", "parent":"bmi", "text": "Underweight"},
+    {"id": "bmi.nw", "parent":"bmi", "text": "Normal"},
+    {"id": "bmi.ow", "parent":"bmi", "text": "Overweight"},
+    {"id": "bmi.ob", "parent":"bmi", "text": "Obese"},
+    {"id": "bmi.vo", "parent":"bmi", "text": "Very Obese"},
+    {"id": "bmi.so", "parent":"bmi", "text": "Severely Obese"},
+    {"id": "bmi.uk", "parent":"bmi", "text": "Unknown BMI"},
+    {"id": "t2d", "parent":"clinical", "text": "Type 2 Diabetes", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "t2d.y", "parent":"t2d", "text": "Yes"},
+    {"id": "t2d.n", "parent":"t2d", "text": "No"},
+    {"id": "t2d.uk", "parent":"t2d", "text": "Unknown"},
+    {"id": "bph", "parent":"clinical", "text": "BPH Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bphsurgery", "parent":"bph", "text": "BPH Surgery", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bphsurg.simp", "parent":"bphsurgery", "text": "Simple Prostatectomy"},
+    {"id": "bphsurg.turp", "parent":"bphsurgery", "text": "TURP"},
+    {"id": "bphsurg.uk", "parent":"bphsurgery", "text": "Unknown Surgery"},
+    {"id": "5ari", "parent":"bph", "text": "5ARI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "5ari.y", "parent":"5ari", "text": "Yes 5ARI"},
+    {"id": "5ari.n", "parent":"5ari", "text": "No 5ARI"},
+    {"id": "5ari.uk", "parent":"5ari", "text": "Unknown 5ARI"},
+    {"id": "5aril", "parent":"bph", "text": "5ARI Length (months)", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "5aril.10", "parent":"5aril", "text": "<10mnths 5ARI"},
+    {"id": "5aril.20", "parent":"5aril", "text": "10-20mnths 5ARI"},
+    {"id": "5aril.30", "parent":"5aril", "text": "20+mnths 5ARI"},
+    {"id": "5aril.uk", "parent":"5aril", "text": "Unknown 5ARI"},
+    {"id": "5aril.na", "parent":"5aril", "text": "NA 5ARI"},
+    {"id": "prostatevol", "parent":"clinical", "text": "Prostate Volume", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "prvol.low", "parent":"prostatevol", "text": "Low Volumne"},
+    {"id": "prvol.med", "parent":"prostatevol", "text": "Medium Volume"},
+    {"id": "prvol.hi", "parent":"prostatevol", "text": "High Volume"},
+    {"id": "prvol.vhi", "parent":"prostatevol", "text": "Very High Volume"},
+    {"id": "prvol.uk", "parent":"prostatevol", "text": "Unknown Volume"},
+    {"id": "repo", "parent":"#", "text": "Repository", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "repo.pr", "parent":"repo", "text": "Prostate", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "repo.pr.cry", "parent":"repo.pr", "text": "Pr Cryopreserved Cells"},
+    {"id": "repo.pr.ff", "parent":"repo.pr", "text": "Pr Flash Frozen Tissue"},
+    {"id": "repo.pr.ffpe", "parent":"repo.pr", "text": "Pr FFPE"},
+    {"id": "repo.pr.oct", "parent":"repo.pr", "text": "Pr OCT"},
+    {"id": "repo.bl", "parent":"repo", "text": "Bladder"},
+    {"id": "repo.sv", "parent":"repo", "text": "Seminal Vesicle"},
+    {"id": "repo.vd", "parent":"repo", "text": "Vas Deferencec"},
+    {"id": "repo.ut", "parent":"repo", "text": "Ureter"}
+]
\ No newline at end of file

layouts/custom/contact.html

@@ -7,16 +7,14 @@
 
 <div class="content">
     <p style="text-align: center">
-        Questions about our research or need a tip on one of our protocols?
-        Interested in collaborations? Email us, mention any person, project, or
-        activity of interest,and we will get back to you soon!
+        Questions about our research or need a tip on one of our protocols? Interested in collaborations? Email us,
+        mention any person, project, or activity of interest,and we will get back to you soon!
     </p>
     <hr>
     <div style="text-align: center">
         <iframe
             src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d3353.0540362781526!2d-96.84412528424524!3d32.81733318923467!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x864e9c04b088e599%3A0x2e63ea34f8b2150b!2sUT%20Southwestern%20Medical%20Center!5e0!3m2!1sen!2sus!4v1576207208811!5m2!1sen!2sus"
-            width="600" height="450" frameborder="0" style="border:0"
-            allowfullscreen=""></iframe>
+            width="600" height="450" frameborder="0" style="border:0" allowfullscreen=""></iframe>
     </div>
     <hr>
     <div style="text-align: center">

layouts/custom/hu.donor.deep.html

@@ -160,19 +160,19 @@
         $(function () {
             var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
             var selectedGene = $("#gene").autocomplete({
-              source: genes.genes,
-              maxResults: 10,
-              maxShowItems: 10,
-              minLength: 1,
+                source: genes.genes,
+                maxResults: 10,
+                maxShowItems: 10,
+                minLength: 1,
             });
-          });
-          $("#analysis").click(function (event) {
+        });
+        $("#analysis").click(function (event) {
             event.preventDefault();
             var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
             _gene = $("#gene").val().toUpperCase();
             if ($.inArray(_gene, genes.genes) < 0) {
-              alert("Gene " + _gene + " not exist in the data.")
-              return
+                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()
@@ -186,6 +186,6 @@
             var img = document.getElementById("img.ViolinBox");
             img.src = "https://s3.us-east-2.amazonaws.com/images.gse117403.deep/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
             return (_gene)
-          });
+        });
     </script>
 </head>
\ No newline at end of file

layouts/custom/hu.donor.shallow.html

 {{ partial "header.html" . }}
 
 <div class="header">
-  <h1>{{ .Title }}</h1>
-  <h2>{{ .Description }}</h2>
+    <h1>{{ .Title }}</h1>
+    <h2>{{ .Description }}</h2>
 </div>
 <div class="content">
-  {{ .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;
-  }
+    .content {
+        margin: 0;
+        max-width: none;
+    }
 
-  img {
-    max-width: 100%;
-    height: auto;
-  }
+    .select {
+        float: top;
+        z-index: 1;
+        top: 0px;
+        background: #191818;
+        overflow-x: hidden;
+        padding: 8px 10px;
+    }
 
-  @media (max-width: 1000px) {
     .columnS {
-      text-align: right;
-      width: 100%;
+        float: left;
+        text-align: center;
+        width: 50%;
     }
 
     .columnF {
-      width: 100%;
+        float: left;
+        text-align: center;
+        width: 33.33%;
+    }
+
+    .row:after {
+        content: "";
+        display: table;
+        clear: both;
     }
 
-    br {
-      display: none;
+    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 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 class="img">
-          <img id="img.ClusterVis" src="" />
+    <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>
-        <br>
-    </div>
-    <div class="columnF">
-      <h4 id="label.Feature">
-        </h3>
-        <div class="img">
-          <img id="img.Feature" src="" />
+        <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 class="columnF">
-      <h4 id="label.ViolinBox">
-        </h3>
-        <div class="img">
-          <img id="img.ViolinBox" src="" />
+    <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>
-        <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>
+    <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_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>
+    <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>
 </head>
\ No newline at end of file

layouts/custom/people.html

@@ -10,18 +10,22 @@
         .column {
             float: left;
         }
+
         .left {
             width: 25%;
         }
+
         .right {
             width: 75%;
         }
+
         .row:after {
             content: "";
             display: table;
             clear: both;
         }
     }
+
     img.pic {
         width: 175px;
         padding: 7px;

layouts/custom/publications.html

@@ -5,12 +5,15 @@
         .column {
             float: left;
         }
+
         .left {
             width: 25%;
         }
+
         .right {
             width: 75%;
         }
+
         .row:after {
             content: "";
             display: table;
@@ -26,35 +29,33 @@
     <br>
     <div>
         {{ range first 10 (.Pages.ByParam "odate" ).Reverse }}
-            <div class="row">
-                <div class="column left">
-                    <img src="images/{{.Params.ppic}}" alt="" width="100px;"
-                        style="border:5px double black; border-radius:20%;">
-                </div>
-                <div class="column right">
-                    <h3>{{.Params.pname}}</h3>
-                </div>
+        <div class="row">
+            <div class="column left">
+                <img src="images/{{.Params.ppic}}" alt="" width="100px;"
+                    style="border:5px double black; border-radius:20%;">
+            </div>
+            <div class="column right">
+                <h3>{{.Params.pname}}</h3>
             </div>
-            {{ if not (eq .Params.ppubmed "") }}
-                <h4><i><a
-                    href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}"
-                    target="_blank">
-            {{else}}
-                <h4><i><a href="{{.Params.plink}}">
-            {{end}}
-                {{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
-            {{ range first 1 .Params.prepo }}
-                {{ if not (eq .title "") }}
+        </div>
+        {{ if not (eq .Params.ppubmed "") }}
+        <h4><i><a href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}" target="_blank">
+                    {{else}}
+                    <h4><i><a href="{{.Params.plink}}">
+                                {{end}}
+                                {{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
+                    {{ range first 1 .Params.prepo }}
+                    {{ if not (eq .title "") }}
                     <u>Data Repository:</u><br>
-                {{end}}
-            {{end}}
-            {{ range .Params.prepo }}
-                {{ if not (eq .title "") }}
+                    {{end}}
+                    {{end}}
+                    {{ range .Params.prepo }}
+                    {{ if not (eq .title "") }}
                     <a href="{{.loc}}" target="_blank">{{.title}}</a><br>
-                {{end}}
-            {{end}}
-            <hr><br>
-        {{end}}
+                    {{end}}
+                    {{end}}
+                    <hr><br>
+                    {{end}}
     </div>
 </div>
 

layouts/custom/research.html

@@ -11,28 +11,33 @@
         display: table;
         clear: both;
     }
+
     div.fig {
         padding: 1px;
         border: 1px solid black;
         margin: auto;
         background-color: LightGrey;
     }
+
     div.fig img {
         width: 500px;
         max-width: 100%;
         height: auto;
         padding: 1px;
     }
+
     div.lab {
         text-align: justify;
         padding-left: 10px;
         padding-right: 10px;
     }
+
     @media (min-width: 1000px) {
         div.fig {
             float: left;
             margin: 1px 10px 1px 1px;
         }
+
         br {
             display: none;
         }
@@ -42,41 +47,30 @@
     <div class="section">
         <H1 align="center">Overview</H1>
         <p style="text-align:justify; font-size:18px">
-            The main goals of the Strand lab are to create accurate cellular
-            atlases of the human and mouse lower
-            urinary tract, characterize the molecular and cellular alterations
-            in human lower urinary tract disease, and
+            The main goals of the Strand lab are to create accurate cellular atlases of the human and mouse lower
+            urinary tract, characterize the molecular and cellular alterations in human lower urinary tract disease, and
             build appropriate models of the human disease in novel mouse models.
         </p>
     </div>
     <div class="section">
         <H1 align="center">Benign Prostatic Hyperplasia</H1>
         <div class="fig" style="max-width:250px">
-            <img src="/research.images/prostate.jpg" alt="prostate" class="img"
-                />
+            <img src="/research.images/prostate.jpg" alt="prostate" class="img" />
             <div class="lab">
-                <p>Cross-section of a prostate gland, showing the transition
-                    zone (TZ) and the peripheral zone (PZ)</p>
+                <p>Cross-section of a prostate gland, showing the transition zone (TZ) and the peripheral zone (PZ)</p>
             </div>
             <p class="br"></p>
         </div>
         <p style="text-align:justify; font-size:18px">
-            A goal of the Strand laboratory is to understand the cellular and
-            molecular biology of lower urinary tract
-            symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder
-            dysfunction. BPH/LUTS is present in the
-            vast majority of men over 70 years old resulting in medical
-            treatment or surgical intervention.
+            A goal of the Strand laboratory is to understand the cellular and molecular biology of lower urinary tract
+            symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder dysfunction. BPH/LUTS is present in the
+            vast majority of men over 70 years old resulting in medical treatment or surgical intervention.
         </p>
         <p style="text-align:justify; font-size:18px">
-            We focus on translational questions related to progression of
-            BPH/LUTS in order to develop new targets for
-            therapeutic intervention. In particular, we are interested in
-            characterizing the cellular composition of
-            particular phenotypes that are resistant to current therapies. We
-            use a combination of single cell RNA
-            sequencing, flow cytometry and immunohistochemistry on normal and
-            diseased human specimens to build a
+            We focus on translational questions related to progression of BPH/LUTS in order to develop new targets for
+            therapeutic intervention. In particular, we are interested in characterizing the cellular composition of
+            particular phenotypes that are resistant to current therapies. We use a combination of single cell RNA
+            sequencing, flow cytometry and immunohistochemistry on normal and diseased human specimens to build a
             cellular atlas of prostate and bladder disease.
         </p>
     </div>
@@ -84,82 +78,56 @@
     <div class="section">
         <H1 align="center">Pathological Heterogeneity in BPH</H1>
         <div class="fig" style="max-width:500px">
-            <img src="/research.images/pheno.jpg" alt="phenotypes" class="img"
-                />
+            <img src="/research.images/pheno.jpg" alt="phenotypes" class="img" />
             <div class="lab">
-                <p>Phenotypic diversity in BPH. Left: glandular enlargement.
-                    Middle: Stromal enlargement. Right: Mixed
+                <p>Phenotypic diversity in BPH. Left: glandular enlargement. Middle: Stromal enlargement. Right: Mixed
                     type.</p>
             </div>
         </div>
         <p style="text-align:justify; font-size:18px">
-            We believe that the basis for heterogeneous clinical responses in
-            BPH is pathologic diversity. There are a
-            number of phenotypes evident across and even within patients. In one
-            area, a patient can display a stromal
+            We believe that the basis for heterogeneous clinical responses in BPH is pathologic diversity. There are a
+            number of phenotypes evident across and even within patients. In one area, a patient can display a stromal
             tumor while the other area display an epithelial nodule.
         </p>
         <p style="text-align:justify; font-size:18px">
-            Our goal is to provide a rational basis for therapeutically treating
-            these individual phenotypes by
-            dissecting them macroscopically and then comparing their
-            cell-specific molecular profiles to reduce the
-            noise of cellular heterogeneity and inflammation. Our first goal is
-            to identify a cell or cells of origin
-            for the varying phenotypes by phenotyping the tissues with single
-            cell RNA sequencing. This includes a
-            comprehensive evaluation of the immune and inflammatory infiltrate
-            as well as fluctuations in epithelial and
+            Our goal is to provide a rational basis for therapeutically treating these individual phenotypes by
+            dissecting them macroscopically and then comparing their cell-specific molecular profiles to reduce the
+            noise of cellular heterogeneity and inflammation. Our first goal is to identify a cell or cells of origin
+            for the varying phenotypes by phenotyping the tissues with single cell RNA sequencing. This includes a
+            comprehensive evaluation of the immune and inflammatory infiltrate as well as fluctuations in epithelial and
             stromal subpopulations.
         </p>
         <p style="text-align:justify; font-size:18px">
-            We are subsequently isolating the cell types of interest and
-            performing molecular profiling. Based on these
-            targets, we will use our mouse and cell culture models to
-            experimentally test our hypotheses.
+            We are subsequently isolating the cell types of interest and performing molecular profiling. Based on these
+            targets, we will use our mouse and cell culture models to experimentally test our hypotheses.
         </p>
     </div>
 
     <div class="section">
         <H1 align="center">Clinical Heterogeneity in BPH</H1>
         <p style="text-align:justify; font-size:18px">
-            It is clear from clinical trials of medications for BPH that
-            personalized therapies will be needed due to
-            the highly variable responses. Typically, patients complaining of
-            lower urinary tract symptoms are placed on
-            an alpha-adrenergic receptor blocker as a first line therapy due to
-            its fast-acting relief of symptoms.
-            These drugs relieve smooth muscle tone and are most effective in
-            patients with early stage disease
-            displaying a high smooth muscle to epithelial tissue composition.
-            However, as the prostate enlarges,
-            epithelial nodules predominate the tissue decreasing the likelihood
-            of alpha-blocker efficacy.
+            It is clear from clinical trials of medications for BPH that personalized therapies will be needed due to
+            the highly variable responses. Typically, patients complaining of lower urinary tract symptoms are placed on
+            an alpha-adrenergic receptor blocker as a first line therapy due to its fast-acting relief of symptoms.
+            These drugs relieve smooth muscle tone and are most effective in patients with early stage disease
+            displaying a high smooth muscle to epithelial tissue composition. However, as the prostate enlarges,
+            epithelial nodules predominate the tissue decreasing the likelihood of alpha-blocker efficacy.
         </p>
         <p style="text-align:justify; font-size:18px">
-            The second-line therapy for BPH is a 5 alpha reductase inhibitor
-            (5ARI), which induces epithelial apoptosis
-            by decreasing the levels of intra-prostatic dihyrotestosterone
-            (DHT). This therapy is effective at reducing
+            The second-line therapy for BPH is a 5 alpha reductase inhibitor (5ARI), which induces epithelial apoptosis
+            by decreasing the levels of intra-prostatic dihyrotestosterone (DHT). This therapy is effective at reducing
             prostate size by 25 percent in most patients.
         </p>
         <p style="text-align:justify; font-size:18px">
-            Importantly, either therapy only reduces symptomatic progression by
-            34 percent, suggesting
-            androgen-independent mechanisms of prostate growth and symptoms need
-            to be targeted. Responses to current
-            drugs are further reduced in patients with obesity, diabetes, and
-            dyslipidemia.
+            Importantly, either therapy only reduces symptomatic progression by 34 percent, suggesting
+            androgen-independent mechanisms of prostate growth and symptoms need to be targeted. Responses to current
+            drugs are further reduced in patients with obesity, diabetes, and dyslipidemia.
         </p>
         <p style="text-align:justify; font-size:18px">
-            These data suggest that there are further measures that are
-            necessary for every patient, and completely
-            novel measures necessary for individual patients. Our goal is to
-            characterize the cellular composition of
-            particular phenotypes, and more deeply understand the molecular
-            changes driving these phenotypes. We use a
-            combination of single cell RNA sequencing, flow cytometry, and
-            immunohistochemistry on specimens from young
+            These data suggest that there are further measures that are necessary for every patient, and completely
+            novel measures necessary for individual patients. Our goal is to characterize the cellular composition of
+            particular phenotypes, and more deeply understand the molecular changes driving these phenotypes. We use a
+            combination of single cell RNA sequencing, flow cytometry, and immunohistochemistry on specimens from young
             organ donors and older men with prostatic enlargement.
         </p>
     </div>

layouts/custom/sc.data.html

 {{ partial "header.html" . }}
 
 <div class="header">
-  <h1>{{ .Title }}</h1>
-  <h2>{{ .Description }}</h2>
+    <h1>{{ .Title }}</h1>
+    <h2>{{ .Description }}</h2>
 </div>
 
 <div class="content">
-  {{ range .Pages.ByWeight }}
+    {{ range .Pages.ByWeight }}
     <li><a href="{{.Permalink}}">{{.Params.name}}</a></li>
-  {{ end }}
+    {{ end }}
 </div>
 
 {{ partial "footer.html" . }}
\ No newline at end of file

static/css/sidenavRepository.css

+/* the sidebar menu */
+.sidenav {
+    width: 30% ;
+    position: fixed/* stay in place on scroll */
+   /* z-index:1; /* stay on top*/
+    top : 0; /* stay on top*/
+    left: 0; /* on left side of screen */
+
+    background: #eee;
+    padding-top: 2px;
+    padding-right:2px;
+}
+
+/* Sidenav filters */
+.sidenav a, .dropdown-btn {
+  padding: 6px 6px 6px 6px;
+  text-decoration: none;
+  color: #818181;
+  display: block;
+  border: none;
+  background: none;
+  width:100%;
+  text-align: left;
+  cursor: pointer;
+  outline: none;
+}
+
+.numbers {
+ text-align: right;
+ padding: 0px 0px 0px 0px;
+ float: right;
+}
+
+#filter {
+ padding-left: 15px;
+ font-size: 85%; 
+ clear: left;
+}
+
+
+/* On mouse-over */
+.sidenav a:hover, .dropdown-btn:hover {
+  color:  #cacfd2  ;
+} 
+
+
+/* Add an active class to the active dropdown button */
+.active {
+  background-color: #909497  ;
+  color: white;
+}
+
+/*change style of sidebar on smaller screens */
+@media screen and (max-height:450px){
+    .sidenav {padding-top: 15px;}
+    .sidenav a {font-size: 18px;}
+}
+
+

static/js/repositoryJS.js

+//$(document).ready(function(){
+
+
+//* Loop through all dropdown buttons to toggle between hiding and showing its dropdown content - This allows the user to have multiple dropdowns without any conflict */
+var dropdown = document.getElementsByClassName("dropdown-btn");
+var i;
+
+for (i = 0; i < dropdown.length; i++) {
+  dropdown[i].addEventListener("click", function() {
+      this.classList.toggle("active");
+          var dropdownContent = this.nextElementSibling;
+              if (dropdownContent.style.display === "block") {
+                    dropdownContent.style.display = "none";
+                        } else {
+                              dropdownContent.style.display = "block";
+                                  }
+                        });
+      }
+
+
+
+/* Get files matching filters
+  
+//declare global vars
+  var results = []; //array of records that match the filters
+  var data = {{ index .Site.Data.scRNAseq_huPr_D.updated_cleaned_json }};
+  var numbers = $("#filter").find(".numbers"); //array of all the places we want to update with the # of records that match the filters
+  var filters = [];//array of current filters
+
+  //filtering function
+  $("input").click(function(){
+
+    // get specific vars
+    var name = $(this).attr("name");
+    var value = $(this).attr("value");
+    var id = name + value;
+    id= id.replace(/\s+/g, '');
+    var filterVar = {"name": name, "value":value, "id":id};
+
+    // if checkbox is checked: add filter values to filter  
+    if ($(this).prop("checked") == true){
+     filters.push(filterVar);
+
+     /* var i;
+      for (i =0; i < data.length; i++){
+         if( data[i][name] == value){
+           results.push(data[i]);
+           $("#"+id).text[numbers.length];
+         }    
+      }*/
+  /*  }
+
+   //if checkbox is not checked: remove filter values from filter 
+   else if ($(this).prop("checked") == false){
+     var i;
+     for (i=0; i<filter.length; i++){
+        if (filter[i][id]== id){
+           filter.splice(i, 1);
+           i--;     
+        }
+     } 
+   } 
+
+   //check data to pull all records that match the current filters
+   var i;
+   var j;
+   for (i = 0; i<filters.length; i++){
+       var count = 0;
+       $('#displayFiles').text(numbers.length);
+                                         
+       for (j=0; j <data.length; j++){
+          //  var id2 = results[j][name]. + results[j][name];
+         // id2 = id2.replace(/\s+/g, '');
+        //   $('#displayFiles').text(id2);
+           if (id2 == numbers[i][id]){
+               count++;
+              $('#displayFiles').text(count);
+           }      
+       }
+   }  
+ });
+});
+*/