update angles and hjust of vertices in Circular Dendrogram

339-circular-dendrogram-with-ggraph.Rmd

@@ -70,14 +70,14 @@ vertices$id=NA
 myleaves=which(is.na( match(vertices$name, edges$from) ))
 nleaves=length(myleaves)
 vertices$id[ myleaves ] = seq(1:nleaves)
-vertices$angle= 90 - 360 * vertices$id / nleaves
+vertices$angle = 360 / nleaves * vertices$id + 110
 
 # calculate the alignment of labels: right or left
 # If I am on the left part of the plot, my labels have currently an angle < -90
-vertices$hjust<-ifelse( vertices$angle < -90, 1, 0)
+vertices$hjust<-ifelse( vertices$angle < 291, 1, 0)
 
 # flip angle BY to make them readable
-vertices$angle<-ifelse(vertices$angle < -90, vertices$angle+180, vertices$angle)
+vertices$angle<-ifelse(vertices$angle < 291, vertices$angle+180, vertices$angle)
 
 # Create a graph object
 mygraph <- graph_from_data_frame( edges, vertices=vertices )
@@ -95,7 +95,8 @@ ggraph(mygraph, layout = 'dendrogram', circular = TRUE) +
     legend.position="none",
     plot.margin=unit(c(0,0,0,0),"cm"),
   ) +
-  expand_limits(x = c(-1.3, 1.3), y = c(-1.3, 1.3))
+  expand_limits(x = c(-1.3, 1.3), y = c(-1.3, 1.3)) +
+  coord_flip()
 ```
 </div>
 </div>

libs/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

libs/navigation-1.1/codefolding.js

@@ -17,13 +17,13 @@ window.initializeCodeFolding = function(show) {
   var currentIndex = 1;
 
   // select all R code blocks
-  var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia');
+  var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia, pre.foldable');
   rCodeBlocks.each(function() {
 
     // create a collapsable div to wrap the code in
     var div = $('<div class="collapse r-code-collapse"></div>');
-    if (show)
-      div.addClass('in');
+    show = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide');
+    if (show) div.addClass('in');
     var id = 'rcode-643E0F36' + currentIndex++;
     div.attr('id', id);
     $(this).before(div);

libs/tocify-1.9.1/jquery.tocify.css

@@ -11,8 +11,6 @@
     margin-left: 2%;
     position: fixed;
     border: 1px solid #ccc;
-    webkit-border-radius: 6px;
-    moz-border-radius: 6px;
     border-radius: 6px;
 }
 
@@ -45,11 +43,15 @@
 .tocify-subheader .tocify-subheader {
     text-indent: 30px;
 }
-
-/* Further indents third level subheader elements. You can continue this pattern if you have more nested elements. */
 .tocify-subheader .tocify-subheader .tocify-subheader {
     text-indent: 40px;
 }
+.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader {
+    text-indent: 50px;
+}
+.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader {
+    text-indent: 60px;
+}
 
 /* Twitter Bootstrap Override Style */
 .tocify .tocify-item > a, .tocify .nav-list .nav-header {

libs/tocify-1.9.1/jquery.tocify.js

@@ -386,13 +386,13 @@
 
           item.append($("<a/>", {
 
-            "text": self.text()
+            "html": self.html()
 
           }));
 
         } else {
 
-          item.text(self.text());
+          item.html(self.html());
 
         }