# HG changeset patch
# User mingchen0919
# Date 1543555409 18000
# Node ID 467a1895c7181fc6d93b1ea519ea88ee2fb16c6a
# Parent  0958dc26c5ae763b23628132e020395a91e281d2
planemo upload commit bd7e129777e3ef6403f055251e17b541d222d7d0-dirty

diff -r 0958dc26c5ae -r 467a1895c718 01_htseq_count_analysis.Rmd
--- a/01_htseq_count_analysis.Rmd	Sat Jun 09 22:29:36 2018 -0400
+++ b/01_htseq_count_analysis.Rmd	Fri Nov 30 00:23:29 2018 -0500
@@ -19,13 +19,13 @@
 
 ## Counts
 
-Only the first few rows are displayed. 
+Write data into a CSV file.
 
-```{r, echo=FALSE}
+```{r, echo=TRUE}
 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
 sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
 colnames(count_data) = rep(sample_names, length = ncol(count_data))
-kable(head(count_data))
+
 
 # modify column names
 count_data = data.frame(feature_id = rownames(count_data), count_data)
@@ -34,3 +34,14 @@
           quote = FALSE, row.names = FALSE)
 ```
 
+Display the top 1000 rows with largest average counts.
+
+```{r echo=TRUE}
+# Sort count table by count average
+rownames(count_data) = count_data$feature_id
+count_data = count_data[, -1]
+sorted_ct_table = count_data[order(rowMeans(count_data), decreasing = TRUE), ]
+DT::datatable(head(sorted_ct_table, 1000))
+```
+
+
diff -r 0958dc26c5ae -r 467a1895c718 index.Rmd
--- a/index.Rmd	Sat Jun 09 22:29:36 2018 -0400
+++ b/index.Rmd	Fri Nov 30 00:23:29 2018 -0500
@@ -28,6 +28,24 @@
 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
 
 ```{r, eval=FALSE, echo=FALSE}
+# The script below is used to avoid conflicts between different javascript labraries
+```
+
+<script>
+jQuery.noConflict();
+ 
+jQuery( document ).ready(function( $ ) {
+    // You can use the locally-scoped $ in here as an alias to jQuery.
+    $( "jstree" ).hide();
+});
+
+// The $ variable in the global scope has the prototype.js meaning.
+window.onload = function(){
+    var mainDiv = $( "main" );
+}
+</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
diff -r 0958dc26c5ae -r 467a1895c718 rmarkdown_report.xml
--- a/rmarkdown_report.xml	Sat Jun 09 22:29:36 2018 -0400
+++ b/rmarkdown_report.xml	Fri Nov 30 00:23:29 2018 -0500
@@ -6,7 +6,8 @@
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
         <requirement type="package" version="1.6">r-rmarkdown</requirement>
-        <requirement type="package" version="0.9.1">htseq</requirement>
+        <requirement type="package" version="0.11.0">htseq</requirement>
+        <requirement type="package" version="0.4">r-dt</requirement>
     </requirements>
     <command><![CDATA[