plot updates

SoniaRuiz · Oct 27, 2020 · c0eacbb · c0eacbb
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diff --git a/.vs/CoExp_Web/v16/.suo b/.vs/CoExp_Web/v16/.suo
diff --git a/CoExp_Web.csproj b/CoExp_Web.csproj
@@ -20,14 +20,17 @@
     <Content Remove="wwwroot\js\Blob.js" />
     <Content Remove="wwwroot\js\canvas-toBlob.js" />
     <Content Remove="wwwroot\js\coexp_menu_data.json" />
+    <Content Remove="wwwroot\js\cytoscape.js" />
     <Content Remove="wwwroot\js\dependent_dropdown.js" />
     <Content Remove="wwwroot\js\eqtl_view.js" />
     <Content Remove="wwwroot\js\excelexportjs.js" />
     <Content Remove="wwwroot\js\FileSaver.js" />
+    <Content Remove="wwwroot\js\pdfmake.min.js" />
     <Content Remove="wwwroot\js\plugins.js" />
     <Content Remove="wwwroot\js\shim.min.js" />
     <Content Remove="wwwroot\js\site.js" />
     <Content Remove="wwwroot\js\site.min.js" />
+    <Content Remove="wwwroot\js\vfs_fonts.js" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/Views/Run/About.cshtml b/Views/Run/About.cshtml
@@ -43,15 +43,15 @@
             <br /><h4>DEVELOPERS</h4><br />
             <p>
                 The User Interface (UI) of CoExp WebPage has been fully developed by <a href="https://rytenlab.com/RytenLab/MemberInfo?Id=LO96_F34158" target="_blank" title="Link to visit Sonia García-Ruiz profile">Sonia García-Ruiz</a>.
-                She is a Ph.D. student, part of the <a href="https://rytenlab.com/RytenLab/" target="_blank" title="Link to visit RytenLab group webpage">RytenLab</a> group, and the WebMaster of CoExp WebPage. For any queries and suggestions related to the CoExp WebPage,
+                She is a Ph.D. student, part of the <a href="https://rytenlab.com/" target="_blank" title="Link to visit RytenLab group webpage">RytenLab</a> group, and the WebMaster of CoExp WebPage. For any queries and suggestions related to the CoExp WebPage,
                 you can reach Sonia at <a href="mailto:[email protected]">s.ruiz@ucl.ac.uk</a>.
                 <br />
                 On the other hand, CoExp R suit-of-packages has been fully developed by <a href="https://rytenlab.com/RytenLab/MemberInfo?Id=BP98-F74160" target="_blank" title="Link to visit Juan A. Botía profile">Juan A. Botía</a>.
                 He is also a member of the Ryten Lab group and Professor at the University of Murcia. You can reach Prof. Botía at <a href="mailto:[email protected]">juanbotiablaya@gmail.com</a>.
                 In addition, Juan A. Botía coordinates the hosting of CoExp Website, which is fully allocated at the <a href="http://www.um.es" target="_blank">University of Murcia</a>.
                 <br />
                 Finally, the brain behind this whole idea and the person who made this software possible is <a href="https://rytenlab.com/RytenLab/MemberInfo?Id=8774A_!52101" target="_blank" title="Link to visit Mina Ryten profile">Mina Ryten</a>,
-                a co-expression network guru and the head of the <a href="https://rytenlab.com/RytenLab/" target="_blank" title="Link to visit RytenLab group webpage">RytenLab</a> group.
+                a co-expression network guru and the head of the <a href="https://rytenlab.com/" target="_blank" title="Link to visit RytenLab group webpage">RytenLab</a> group.
             </p>
 
             <br /><h4>COEXP ON GITHUB</h4><br />

diff --git a/Views/Run/Annotated.cshtml b/Views/Run/Annotated.cshtml
@@ -355,8 +355,9 @@
     <script type="text/javascript" src="~/js/buttons.html5.min.js"></script>
     <script type="text/javascript" src="~/js/buttons.print.min.js"></script>
     <script type="text/javascript" src="~/js/jszip.min.js"></script>
-    <script type="text/javascript" src="~/js/pdfmake.min.js"></script>
-    <script type="text/javascript" src="~/js/vfs_fonts.js"></script>
+    @*<script type="text/javascript" src="~/js/pdfmake.min.js"></script>*@
+    <script type="text/javascript" src="~/lib/pdfmake/pdfmake.min.js"></script>
+    <script type="text/javascript" src="~/lib/pdfmake/vfs_fonts.min.js"></script>
 
     <script>
         $(document).ready(function () {

diff --git a/Views/Run/Catalogue.cshtml b/Views/Run/Catalogue.cshtml
@@ -1,7 +1,7 @@
 @model CoexpParams
 @{
     //View of the main page
-    ViewData["Title"] = "Network Catalog";
+    ViewData["Title"] = "Network Catalogue";
 }
 
 @Html.HiddenFor(m => m.Category)
@@ -10,23 +10,23 @@
 @Html.HiddenFor(m => m.Genes)
 
 
-    <div class="breadcrumb">
-        @if (ViewContext.RouteData.Values["controller"].ToString() != "Home")
-        {
-            <span class="main-label-breadcrumbs">CoExp</span>@*@Html.ActionLink(ViewContext.RouteData.Values["controller"].ToString(), "Index", ViewContext.RouteData.Values["controller"].ToString())*@
-            <span class="glyphicon glyphicon-chevron-right"></span>
-        }
-        @if (ViewContext.RouteData.Values["action"].ToString() != "Index")
-        {
-            <span class="active">Network Catalogue</span>
-            @*@if (Model.ModuleColor != null)
+<div class="breadcrumb">
+    @if (ViewContext.RouteData.Values["controller"].ToString() != "Home")
+    {
+        <span class="main-label-breadcrumbs">CoExp</span>@*@Html.ActionLink(ViewContext.RouteData.Values["controller"].ToString(), "Index", ViewContext.RouteData.Values["controller"].ToString())*@
+        <span class="glyphicon glyphicon-chevron-right"></span>
+    }
+    @if (ViewContext.RouteData.Values["action"].ToString() != "Index")
+    {
+        <span class="active">Network Catalogue</span>
+        @*@if (Model.ModuleColor != null)
             {
                 <span class="active">Network Catalogue</span>
             }else {
                 @Html.ActionLink("Network Catalogue", ViewContext.RouteData.Values["action"].ToString(), ViewContext.RouteData.Values["controller"].ToString())
             }*@
-        }
-    </div>
+    }
+</div>
 <div class="row">
     <div id="menu" class="col-sm-3 sidebar menu">
         <div id="menu_gene_list" class="hidden">
@@ -42,11 +42,11 @@
             <div id="step1">
                 <label for="category_dropdown">Category</label>
                 <i class="glyphicon glyphicon-info-sign"
-                    data-toggle="tooltip"
-                    data-placement="right"
-                    data-html="true"
-                    title="<br/><p>CATEGORY</p><hr/><ul style='text-align: left;'> <li>ROSMAP, contains 4 case and control Frontal Cortex co-expression networks;</li><br/><li>GTEx V6, contains 47 co-expression networks in control tissue;</li><br/><li>10UKBEC, contains 10 Illumina microarray-based gene expression profiling networks from brain control tissue;</li><br/><li>GTEx V7, contains a beta version of the same 47 co-expression networks from GTExV6;</li><br/><li>NABEC, contains 1 gene co-expression network created from RNA-seq control Cortex samples.</li></ul>"
-                    style="vertical-align: middle;"></i>
+                   data-toggle="tooltip"
+                   data-placement="right"
+                   data-html="true"
+                   title="<br/><p>CATEGORY</p><hr/><ul style='text-align: left;'> <li>ROSMAP, contains 4 case and control Frontal Cortex co-expression networks;</li><br/><li>GTEx V6, contains 47 co-expression networks in control tissue;</li><br/><li>10UKBEC, contains 10 Illumina microarray-based gene expression profiling networks from brain control tissue;</li><br/><li>GTEx V7, contains a beta version of the same 47 co-expression networks from GTExV6;</li><br/><li>NABEC, contains 1 gene co-expression network created from RNA-seq control Cortex samples.</li></ul>"
+                   style="vertical-align: middle;"></i>
                 <br />
                 <select id="category_dropdown" name="category" class="selectpicker" title="Select an option ...">
                     @*<option></option>*@
@@ -105,9 +105,10 @@
                 <div id="goFromTissue_div" style="display:none">
                     <h2>Ontology view</h2>
                     <p>
-                        The data table below displays in the rows all modules that belong to the co-expression network selected. On the other hand, the columns provide information related to the ontology term that more strongly correlates with the genes clustered within each module.
-                        The p-value column supports the overlap between the ontology term returned and the genes clustered in the current module. 
-                        The raw data that supports the generation of this data table is available to be downloaded under the three buttons placed on the upper-left-side corner of the table.
+                        The datatable below displays data in rows and columns, with one row for each module belonging to the co-expression network selected. The columns provide information related to the 
+                        ontology term that more strongly correlates with the genes clustered within each module.
+                        The p-value column supports the overlap between the ontology term returned and the genes clustered within the current module.
+                        The raw data behind the generation of this data table is available to be downloaded on the three buttons placed on the upper-left-side corner of the table.
                     </p>
                     <br>
                     <table id="goFromTissue_table" class="table table-striped table-bordered wrap"></table>
@@ -123,9 +124,9 @@
                 <div id="cellType_div" style="display:none;">
                     <h2>Cell Type view</h2>
                     <p>
-                        The data table below displays in the columns all modules that belong to the co-expression network selected. On the other hand, the rows contain the different cell types.
+                        The datatable below displays in the columns all modules that belong to the co-expression network selected. The rows contain information associated to the different cell types.
                         The intersection between each row and column contains a p-value, corrected by the Bonferroni method, that supports the linkage between each cell type and all genes found in the corresponding module.
-                        The raw data that supports the generation of this data table is available to be downloaded under the three buttons placed on the upper-left-side corner of the table.
+                        The raw data supporting the generation of this data table is available to be downloaded under the three buttons placed on the upper-left-side corner of the table.
                     </p>
                     <br>
                     <table id="cellType_table" class="table table-striped table-bordered nowrap"></table>
@@ -155,9 +156,9 @@
 }
 @section Scripts{
     <script type="text/javascript">
-            // Turn active current menu's option
-            $(".nav-item").find(".active").removeClass("active");
-            $("#tab_network_catalogue").addClass("active");
+        // Turn active current menu's option
+        $(".nav-item").find(".active").removeClass("active");
+        $("#tab_network_catalogue").addClass("active");
     </script>
 
     <script type="text/javascript" src="~/js/underscore-min.js"></script>
@@ -175,8 +176,8 @@
     <script type="text/javascript" src="~/js/dataTables.buttons.min.js"></script>
     <script type="text/javascript" src="~/js/buttons.flash.min.js"></script>
     <script type="text/javascript" src="~/js/jszip.min.js"></script>
-    <script type="text/javascript" src="~/js/pdfmake.min.js"></script>
-    <script type="text/javascript" src="~/js/vfs_fonts.js"></script>
+    <script type="text/javascript" src="~/lib/pdfmake/pdfmake.min.js"></script>
+    <script type="text/javascript" src="~/lib/pdfmake/vfs_fonts.min.js"></script>
     <script type="text/javascript" src="~/js/buttons.html5.min.js"></script>
     <script type="text/javascript" src="~/js/buttons.print.min.js"></script>
     <script type="text/javascript" src="~/js/buttons.colVis.min.js"></script>
@@ -202,10 +203,10 @@
             else {
                 API.prototype.menuInit(11);
             }
-            
+
         });
 
-        
+
       function startIntro(){
         var intro = introJs();
           intro.setOptions({
@@ -215,7 +216,7 @@
                       intro: "<p><b>Category</b></p><p>Please, select here your preferred category of co-expression networks.</p>",
                       position: 'right',
                       scrollTo: 'tooltip'
-                      
+
                   },
                   {
                       element: '#step2',
@@ -255,9 +256,9 @@
                 sessionStorage.setItem('EventTourCatalogue', 'Completed');
             });
         }
-   
+
       }
-    
-        
+
+
     </script>
 }
diff --git a/Views/Run/Help.cshtml b/Views/Run/Help.cshtml
@@ -43,7 +43,7 @@
                 This is the "Getting Started" tutorial. It contains the details of the use-of-case that we are going to use throughout  the whole series.
             </p>
 
-            <br /><h4><a asp-area="" asp-controller="Run" asp-action="Help_Catalogue">NETWORK CATALOG</a></h4><br />
+            <br /><h4><a asp-area="" asp-controller="Run" asp-action="Help_Catalogue">NETWORK CATALOGUE</a></h4><br />
             <p>
                 This is the second tutorial of the series. It contains information about how to use the 'Network Catalogue' tab.
             </p>

diff --git a/Views/Run/Help_Annotation.cshtml b/Views/Run/Help_Annotation.cshtml
@@ -20,12 +20,12 @@
         </p>
         <hr class="menu-hr" />
         <p>This is the third and last part of the tutorial series <a asp-area="" asp-controller="Run" asp-action="Help">"Getting started with CoExp WebPage application"</a>.</p>
-        <p><span class="glyphicon glyphicon-chevron-left"></span><b>Previous: </b><a asp-area="" asp-controller="Run" asp-action="Help_Catalogue">Surfing the Catalog</a></p>
+        <p><span class="glyphicon glyphicon-chevron-left"></span><b>Previous: </b><a asp-area="" asp-controller="Run" asp-action="Help_Catalogue">Surfing the Catalogue</a></p>
 
         <div>
             <br />
             <p>
-                In the <a asp-area="" asp-controller="Run" asp-action="Help_Catalogue">previous</a> tutorial, we explained how to make use of the "Network Catalog" tab.
+                In the <a asp-area="" asp-controller="Run" asp-action="Help_Catalogue">previous</a> tutorial, we explained how to make use of the "Network Catalogue" tab.
                 In this one, we will explain how to use the "Gene Set Annotation" tab.
             </p>
             <p>

diff --git a/Views/Run/Help_Introduction.cshtml b/Views/Run/Help_Introduction.cshtml
@@ -47,7 +47,7 @@
             </blockquote><br />
             <p>
                 Thus, in order to answer the list of questions detailed above, the first thing we have to do is to choose which are the conditions in which we would like to study the genes.
-                For that purpose, we will firstly surf through the network catalogue of genes available within the tab 'Network Catalog' on the CoExp WebPage tool.
+                For that purpose, we will firstly surf through the network catalogue of genes available within the tab 'Network Catalogue' on the CoExp WebPage tool.
             </p>
             <br />