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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:48:14 -0500
parents b7c115edd970
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1:92e3de11b9f8 2:c64267b9f754
1 ---
2 title: "FastQC Report"
3 output: html_document
4 ---
5 1
6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} 2
7 knitr::opts_chunk$set(echo = TRUE, error = TRUE) 3 ```{css, echo=FALSE}
4 pre code, pre, code {
5 white-space: pre !important;
6 overflow-x: scroll !important;
7 word-break: keep-all !important;
8 word-wrap: initial !important;
9 }
8 ``` 10 ```
9 11
12 ```{r, echo=FALSE}
13 # to make the css theme to work, <link></link> tags cannot be added directly
14 # as <script></script> tags as below.
15 # it has to be added using a code chunk with the htmltool functions!!!
16 css_link = tags$link()
17 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
18 css_link
19 ```
20
21 ```{r, eval=FALSE, echo=FALSE}
22 # this code chunk is purely for adding comments
23 # below is to add jQuery and jstree javascripts
24 ```
25
26 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
10 27
11 28
12 ## References 29 ```{r, eval=FALSE, echo=FALSE}
30 # this code chunk is purely for adding comments
31 # javascript code below is to build the file tree interface
32 # see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
33 ```
34 <script>
35 jQuery(function () {
36 // create an instance when the DOM is ready
37 jQuery('#jstree').jstree().bind("select_node.jstree", function (e, data) {
38 window.open( data.node.a_attr.href, data.node.a_attr.target )
39 });
40 });
41 </script>
13 42
14 * Bioinformatics, Babraham (2014). FastQC. 43 ## Outputs
15 44
16 * Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob (2016). rmarkdown: Dynamic Documents for R, 2016. In R package version 0.9, 6. 45 ```{r, echo=FALSE}
17 46 # create a div container to store the file tree interface
18 * Xie, Yihui (2015). Dynamic Documents with R and knitr, CRC Press, Vol.29. 47 tags$div(
19 48 id="jstree",
20 * Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. [Link] 49 file_tree(Sys.getenv('REPORT_FILES_PATH'))
21 50 )
22 * Wickham, H. (2016). ggplot2: elegant graphics for data analysis. Springer. Chicago 51 ```