# HG changeset patch
# User mingchen0919
# Date 1544040501 18000
# Node ID d7ff8ae0ca363970e49bd0fe84d3fbfa3d4da862
# Parent  52364533eac50e407d36a9d09efef49e871595ee
planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1

diff -r 52364533eac5 -r d7ff8ae0ca36 rmarkdown_report.Rmd
--- a/rmarkdown_report.Rmd	Wed Dec 05 12:42:57 2018 -0500
+++ b/rmarkdown_report.Rmd	Wed Dec 05 15:08:21 2018 -0500
@@ -6,12 +6,10 @@
 ---
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(error = TRUE, echo = TRUE)
+knitr::opts_chunk$set(error = TRUE, echo = FALSE)
 ```
 
-
-```{css echo=FALSE}
-# code chunks scrollable
+```{css, echo=FALSE}
 pre code, pre, code {
   white-space: pre !important;
   overflow-x: scroll !important;
@@ -20,7 +18,6 @@
 }
 ```
 
-
 ```{r, echo=FALSE}
 # to make the css theme to work, <link></link> tags cannot be added directly 
 # as <script></script> tags as below.
@@ -34,22 +31,25 @@
 # this code chunk is purely for adding comments
 # below is to add jQuery and jstree javascripts
 ```
-<script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
+
 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
 
----
+
+```{r, eval=FALSE, echo=FALSE}
+# this code chunk is purely for adding comments
 # javascript code below is to build the file tree interface
 # see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
----
+```
 <script>
-  $(function () {
+  jQuery(function () {
     // create an instance when the DOM is ready
-    $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
+    jQuery('#jstree').jstree().bind("select_node.jstree", function (e, data) {
      window.open( data.node.a_attr.href, data.node.a_attr.target )
     });
   });
 </script>
 
+
 ---
 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
 ---
@@ -84,7 +84,7 @@
 
 ## Differential expression test results
 res = results(dds, contrast = c(opt$X_D, opt$X_E, opt$X_F), alpha = opt$X_I)
-res
+DT::datatable(as.data.frame(res))
 ```