--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_report.Rmd	Thu Dec 13 22:46:23 2018 -0500
@@ -0,0 +1,113 @@
+---
+title: 'HTSeq-count Report'
+output:
+    html_document:
+      highlight: pygments
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(error = TRUE, echo = FALSE)
+```
+
+```{css echo=FALSE}
+# code chunks scrollable
+pre code, pre, code {
+  white-space: pre !important;
+  overflow-x: scroll !important;
+  word-break: keep-all !important;
+  word-wrap: initial !important;
+}
+```
+
+
+```{r, echo=FALSE}
+# to make the css theme to work, <link></link> tags cannot be added directly 
+# as <script></script> tags as below.
+# it has to be added using a code chunk with the htmltool functions!!!
+css_link = tags$link()
+css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
+css_link
+```
+
+```{r, eval=FALSE, echo=FALSE}
+# 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}
+# 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>
+
+---
+# 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 () {
+    // create an instance when the DOM is ready
+    $('#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
+---
+
+## Job script
+
+```{bash, echo=FALSE}
+sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
+```
+
+```{r echo=FALSE, comment='', results='asis'}
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
+cat('\n```')
+```
+
+## Counts
+
+Write data into a CSV file.
+
+```{r, echo=TRUE}
+count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
+sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
+colnames(count_data) = rep(sample_names, length = ncol(count_data))
+
+
+# modify column names
+count_data = data.frame(feature_id = rownames(count_data), count_data)
+write.csv(count_data, 
+          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
+          quote = FALSE, row.names = FALSE)
+```
+
+Display the top 1000 rows with largest average counts.
+
+```{r echo=TRUE}
+# Sort count table by count average
+rownames(count_data) = count_data$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))
+```
+
+