Merge branch 'add.muPrUr' into 'develop'

Add.mu pr ur See merge request !31

Merge branch 'add.muPrUr' into 'develop'
Add.mu pr ur See merge request !31
906d0ebb · Gervaise Henry · 1564eeee · b134d9a2 · 906d0ebb · 906d0ebb
Commit 906d0ebb authored 5 years ago by Gervaise Henry
--- a/archetypes/sc_data.md
+++ b/archetypes/sc_data.md
 ---
 title: "{{ replace .Name "-" " " | title }}"
 description: "Single-Cell RNA-sequencing Data"
 name: "(PENDING)"
 date: {{ .Date }}
 draft: true
 weight: ""
 type: "custom"
 layout: ""
 current: true
 ---
 **PENDING**
\ No newline at end of file
--- a/content/sc.data/hu.donor.pr.deep.md
+++ b/content/sc.data/hu.donor.pr.deep.md
 ---
 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
 ---

--- a/content/sc.data/hu.bph.pr.md
+++ b/content/sc.data/hu.bph.pr.md
---
-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**
\ No newline at end of file
--- a/content/sc.data/hu.cancer.pr.md
+++ b/content/sc.data/hu.cancer.pr.md
---
-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**
\ No newline at end of file
--- a/content/sc.data/hu.donor.pr.shallow.md
+++ b/content/sc.data/hu.donor.pr.shallow.md
---
-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
---
--- a/content/sc.data/mu.bl.md
+++ b/content/sc.data/mu.bl.md
---
-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**
\ No newline at end of file
--- a/content/sc.data/mu.pr.md
+++ b/content/sc.data/mu.pr.md
---
-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**
\ No newline at end of file
--- a/content/sc.data/hu.donor.bl.md
+++ b/content/sc.data/hu.donor.bl.md
 ---
-title: "Human Donor Bladder"
+title: "Mouse Prostate and Urethra"
 description: "Single-Cell RNA-sequencing Data"
-name: "Human Donor Bladder (PENDING)"
+name: "Mouse Prostate and Urethra"
-date: 2019-12-24T22:35:48-06:00
+date: 2020-02-19T23:28:10-06:00
-draft: false
+draft: true
 weight: "3"
 type: "custom"
-layout: ""
+layout: "muPrUr"
-current: false
+current: true
 ---
-**PENDING**
\ No newline at end of file
--- a/data/sc_data/hu_donor_pr_deep/genes.json
+++ b/data/sc_data/hu_donor_pr_deep/genes.json
--- a/data/sc_data/hu_donor_pr_shallow/genes.json
+++ b/data/sc_data/hu_donor_pr_shallow/genes.json
--- a/data/sc_data/mu/genes.json
+++ b/data/sc_data/mu/genes.json
--- a/layouts/custom/hu.donor.deep.html
+++ b/layouts/custom/hu.donor.deep.html
@@ -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 value="Region">Prostatic Region</option>
-                <option>Patient</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="dis">Distal Prostate</option>
-                <option value="st">Stroma Only</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>

--- a/layouts/custom/hu.donor.shallow.html
+++ b/layouts/custom/hu.donor.shallow.html
 {{ partial "header.html" . }}
 <div class="header">
    <h1>{{ .Title }}</h1>
    <h2>{{ .Description }}</h2>
 </div>
+<div class="content">
-<style>
+    {{ .Content }}
-    .content {
+</div>
-        margin: 0;
-        max-width: none;
+<style>
-    }
+    .content {
+        margin: 0;
-    .select {
+        max-width: none;
-        float: top;
+    }
-        z-index: 1;
-        top: 0px;
+    .select {
-        background: #191818;
+        float: top;
-        overflow-x: hidden;
+        z-index: 1;
-        padding: 8px 10px;
+        top: 0px;
-    }
+        background: #191818;
+        overflow-x: hidden;
-    .columnS {
+        padding: 8px 10px;
-        float: left;
+    }
-        text-align: center;
-        width: 50%;
+    .columnS {
-    }
+        float: left;
+        text-align: center;
-    .columnF {
+        width: 33.33%;
-        float: left;
+    }
-        text-align: center;
-        width: 33.33%;
+    .columnF {
-    }
+        float: left;
+        text-align: center;
-    .row:after {
+        width: 33.33%;
-        content: "";
+    }
-        display: table;
-        clear: both;
+    .row:after {
-    }
+        content: "";
+        display: table;
-    img {
+        clear: both;
-        max-width: 100%;
+    }
-        height: auto;
-    }
+    img {
+        max-width: 100%;
-    @media (max-width: 1000px) {
+        height: auto;
-        .columnS {
+    }
-            text-align: right;
-            width: 100%;
+    @media (max-width: 1250px) {
-        }
+        .columnS {
+            text-align: right;
-        .columnF {
+            width: 100%;
-            width: 100%;
+        }
-        }
+        .columnF {
-        br {
+            width: 100%;
-            display: none;
+        }
-        }
-    }
+        br {
-</style>
+            display: none;
+        }
-<div class="content">
+    }
-    <div class="select">
+</style>
-        <div class="columnS ui-widget">
-            <label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
+<div class="content">
-            <br>
+    <div class="select">
-            <input id="gene" size="19">
+        <div class="columnS ui-widget">
-        </div>
+            <label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
-        <div class="columnS">
+            <br>
-            <label for="populations" style="font-size:18px;">
+            <input id="gene" size="19">
-                <b>Select a group of cell populations:</b>
+        </div>
-            </label>
+        <div class="columnS">
-            <br>
+            <label for="populations" style="font-size:18px;">
-            <select name="populations" id="populations">
+                <b>Select a group of cell populations:</b>
-                <option selected="selected" value="Population"> Cell Populations</option>
+            </label>
-                <option>Lineage</option>
+            <br>
-                <option value="Zone">Prostatic Zone</option>
+            <select name="populations" id="populations">
-                <option>Patient</option>
+                <option selected="selected" value="Population">Cell Populations</option>
-            </select>
+                <option>Lineage</option>
-        </div>
+                <option>Tissue</option>
-        <br>
+            </select>
-        <div style="text-align:center">
+        </div>
-            <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
+        <div class="columnS">
-        </div>
+            <label for="group" style="font-size:18px;">
-        <hr>
+                <b>Select a group of cell to display:</b>
-        <div>
+            </label>
-            <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
+            <br>
-            <br>
+            <select name="group" id="group">
-            <span style="font-size:16px;">
+                <option selected="selected" value="all">All Cells</option>
-                Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from
+                <option value="pr">Prostate Only</option>
-                the prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were
+                <option value="ur">Urethra Only</option>
-                clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can
+            </select>
-                be compared by population identity, cell lineage, patient, or dissected prostatic zone. This is the
+        </div>
-                original sequencing depth published.
+        <br>
-            </span>
+        <div style="text-align:left">
-        </div>
+            <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
-    </div>
+        </div>
-    <div align="center">
+        <hr>
-        <h1 id="label.gene">NO GENE SELECTED</h1>
+        <div>
-        <h2 id="label.populations"></h2>
+            <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
-        <div class="columnF">
+            <br>
-            <h4 id="label.ClusterVis">
+            <span style="font-size:16px;">
-                </h3>
+                Single Cell RNA-Sequencing was conducted on C57BL/6 mouse prostates and urethra. The cells were
-                <div data-proofer-ignore class="img">
+                clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can
-                    <img id="img.ClusterVis" src="" />
+                be compared by population identity, cell lineage, or tissue source.
-                </div>
+            </span>
-                <br>
+        </div>
-        </div>
+    </div>
-        <div class="columnF">
+    <div align="center">
-            <h4 id="label.Feature">
+        <h1 id="label.gene">NO GENE SELECTED</h1>
-                </h3>
+        <h2 id="label.populations"></h2>
-                <div data-proofer-ignore class="img">
+        <h3 id="label.group"></h3>
-                    <img id="img.Feature" src="" />
+        <div class="columnF">
-                </div>
+            <h4 id="label.ClusterVis">
-                <br>
+                </h3>
-        </div>
+                <div data-proofer-ignore class="img">
-        <div class="columnF">
+                    <img id="img.ClusterVis" src="" />
-            <h4 id="label.ViolinBox">
+                </div>
-                </h3>
+                <br>
-                <div data-proofer-ignore class="img">
+        </div>
-                    <img id="img.ViolinBox" src="" />
+        <div class="columnF">
-                </div>
+            <h4 id="label.Feature">
-                <br>
+                </h3>
-        </div>
+                <div data-proofer-ignore class="img">
-    </div>
+                    <img id="img.Feature" src="" />
-    <hr>
+                </div>
-    <div align="left">
+                <br>
-        <div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
+        </div>
-        <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
+        <div class="columnF">
-                    target="_blank">Cell Reports</a></span></div>
+            <h4 id="label.ViolinBox">
-        <div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
+                </h3>
-        <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
+                <div data-proofer-ignore class="img">
-                    target="_blank">GEO:
+                    <img id="img.ViolinBox" src="" />
-                    GSE117403</a></span></div>
+                </div>
-        <div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
+                <br>
-                    W-R8CM</a></span></div>
+        </div>
    </div>
-</div>
+    <hr>
+    <div align="left">
-{{ partial "footer.html" . }}
+        <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"
-<head>
+                    target="_blank">bioRxiv</a></span></div>
-    <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
+        <div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
-    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+        <div><span style="font-size:16px;"> <a href="https://doi.org/10.1101/2020.02.19.937615"
-    <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
+                    target="_blank">Mouse Prostate GEO: GSEXXX</a></span></div>
-    <style>
+                    <div><span style="font-size:16px;"> <a href="https://doi.org/10.1101/2020.02.19.937615"
-        .ui-autocomplete {
+                        target="_blank">Mouse Urethra GEO: GSEXXX</a></span></div>
-            max-height: 200px;
+        <div><span style="font-size:16px;"><a href="https://doi.org/10.25548/16-WM8C" target="_blank">GUDMAP:
-            overflow-y: auto;
+            16-WM8C</a></span></div>
-            overflow-x: hidden;
+    </div>
-        }
+</div>
-    </style>
-    <script>
+{{ partial "footer.html" . }}
-        $(function () {
-            $("#populations").selectmenu({ width: 230 });
+<head>
-        });
+    <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
-        $(function () {
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
-            var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
+    <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
-            var selectedGene = $("#gene").autocomplete({
+    <style>
-                source: genes.genes,
+        .ui-autocomplete {
-                maxResults: 10,
+            max-height: 200px;
-                maxShowItems: 10,
+            overflow-y: auto;
-                minLength: 1,
+            overflow-x: hidden;
-            });
+        }
-        });
+    </style>
-        $("#analysis").click(function (event) {
+    <script>
-            event.preventDefault();
+        $(function () {
-            var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
+            $("#populations").selectmenu({ width: 220, height: 1 });
-            _gene = $("#gene").val().toUpperCase();
+        });
-            if ($.inArray(_gene, genes.genes) < 0) {
+        $(function () {
-                alert("Gene " + _gene + " not exist in the data.")
+            $("#group").selectmenu({ width: 220 });
-                return
+        });
-            }
+        $(function () {
-            document.getElementById("label.gene").innerHTML = _gene
+            var genes = {{ index .Site.Data.sc_data.mu.genes }};
-            document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
+            var selectedGene = $("#gene").autocomplete({
-            document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
+                source: genes.genes,
-            var img = document.getElementById("img.ClusterVis");
+                maxResults: 10,
-            img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
+                maxShowItems: 10,
-            document.getElementById("label.Feature").innerHTML = "Feature Plot"
+                minLength: 1,
-            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"
+        $("#analysis").click(function (event) {
-            var img = document.getElementById("img.ViolinBox");
+            event.preventDefault();
-            img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
+            var genes = {{ index .Site.Data.sc_data.mu.genes }};
-            return (_gene)
+            _gene = $("#gene").val().charAt(0).toUpperCase() + $("#gene").val().slice(1).toLowerCase();
-        });
+            if ($.inArray(_gene, genes.genes) < 0) {
-    </script>
+                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