update pkgdown template

geneticsMiNIng · Dec 4, 2017 · 2b9adcb · 2b9adcb
1 parent 4dfd28a
commit 2b9adcb
Show file tree

Hide file tree

Showing 43 changed files with 308 additions and 177 deletions.
diff --git a/MLExpResso/DESCRIPTION b/MLExpResso/DESCRIPTION
@@ -31,7 +31,7 @@ Imports: AnnotationDbi,
     scales, 
     stringr, 
     TxDb.Hsapiens.UCSC.hg18.knownGene,
-    utils, 
+    utils
 RoxygenNote: 6.0.1
 Suggests: knitr,
     MLExpRessoData,

diff --git a/docs/MI2logo.jpg b/docs/MI2logo.jpg
diff --git a/docs/articles/QuickStart.html b/docs/articles/QuickStart.html
diff --git a/docs/articles/QuickStart_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/QuickStart_files/figure-html/unnamed-chunk-11-1.png
diff --git a/docs/articles/QuickStart_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/QuickStart_files/figure-html/unnamed-chunk-3-1.png
diff --git a/docs/articles/QuickStart_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/QuickStart_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
@@ -133,7 +133,7 @@ pre {
 }
 
 pre, code {
-  background-color: #e5e5e5;
+  background-color: #f8f8f8;
   color: #333;
 }
 
@@ -150,6 +150,11 @@ pre .img img {
 code a, pre a {
   color: #375f84;
 }
+table {
+    display: block;
+    overflow: auto;
+	width: 100% !important;
+}
 
 .fl      {color: #1514b5;}
 .fu      {color: #000000;} /* function */
@@ -161,6 +166,44 @@ code a, pre a {
 .error   { color: orange;  font-weight: bolder;}
 .warning { color: #6A0366; font-weight: bolder;}
 
-.navbar-default {
-    background-color: #4a3c89;
+.navbar-mi2logo {
+    float: left;
+	margin-right: 15px;
+	margin-top: 2px;
+}
+.navbar-mi2 {
+	background-color: #4a3c89;
+    color: #fff !important;
+	margin-right: 0px;
+}
+.navbar-mi2 > li > a {
+    color: #fff !important;
+}
+.navbar-mi2 > .active > a{
+    background-color: #370f54 !important;
+}
+.navbar-mi2 > .open > a:focus, .nav-pills> .open > a:focus{
+    background-color: #370f54 !important;
+}
+.dropdown-menu > .active > a, .dropdown-menu > .active > a:focus{
+    background-color: #370f54 !important;
+}
+
+ .contents-mi2 > li > a:focus, .nav-pills > li > a:focus {
+    background-color: #4a3c89 !important;
+	color: #fff;
+}
+ .contents-mi2 > li.active > a, .nav-pills > li.active > a{
+    background-color: #370f54 !important;
+}
+ .contents-mi2 > li > a, .nav-pills > li > a{
+    background-color: #4a3c89 !important;
+	color: #fff;
+}
+
+.sidebar-logo {
+	display:block;
+	margin-left:auto;
+	margin-right:auto;
+	text-align: justify;
 }
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
@@ -5,41 +5,19 @@ $(function() {
     offset: 60
   });
 
-  var cur_path = paths(location.pathname);
+  var cur_path = location.href;
   $("#navbar ul li a").each(function(index, value) {
     if (value.text == "Home")
       return;
     if (value.getAttribute("href") === "#")
       return;
 
-    var path = paths(value.pathname);
-    if (is_prefix(cur_path, path)) {
+	var path = value.href;
+    if (cur_path == path) {
       // Add class to parent <li>, and enclosing <li> if in dropdown
       var menu_anchor = $(value);
       menu_anchor.parent().addClass("active");
       menu_anchor.closest("li.dropdown").addClass("active");
     }
   });
 });
-
-function paths(pathname) {
-  var pieces = pathname.split("/");
-  pieces.shift(); // always starts with /
-
-  var end = pieces[pieces.length - 1];
-  if (end === "index.html" || end === "")
-    pieces.pop();
-  return(pieces);
-}
-
-function is_prefix(needle, haystack) {
-  if (needle.length > haystack.lengh)
-    return(false);
-
-  for (var i = 0; i < haystack.length; i++) {
-    if (needle[i] != haystack[i])
-      return(false);
-  }
-
-  return(true);
-}
diff --git a/docs/reference/aggregate_probes.html b/docs/reference/aggregate_probes.html
diff --git a/docs/reference/calculate_CpG_mean.html b/docs/reference/calculate_CpG_mean.html
diff --git a/docs/reference/calculate_chromosome_data.html b/docs/reference/calculate_chromosome_data.html