|
0
|
1 ---
|
|
|
2 title: 'HTML report title'
|
|
|
3 output:
|
|
|
4 html_document:
|
|
|
5 highlight: pygments
|
|
|
6 ---
|
|
|
7
|
|
|
8 ```{r, echo=FALSE}
|
|
|
9 # to make the css theme to work, <link></link> tags cannot be added directly
|
|
|
10 # as <script></script> tags as below.
|
|
|
11 # it has to be added using a code chunk with the htmltool functions!!!
|
|
|
12 css_link = tags$link()
|
|
|
13 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
|
|
|
14 css_link
|
|
|
15 ```
|
|
|
16
|
|
|
17 ```{r, eval=FALSE, echo=FALSE}
|
|
|
18 # this code chunk is purely for adding comments
|
|
|
19 # below is to add jQuery and jstree javascripts
|
|
|
20 ```
|
|
|
21 <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
|
|
|
22 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
|
|
|
23
|
|
|
24 ```{r, eval=FALSE, echo=FALSE}
|
|
|
25 # this code chunk is purely for adding comments
|
|
|
26 # javascript code below is to build the file tree interface
|
|
|
27 # 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
|
|
|
28 ```
|
|
|
29 <script>
|
|
|
30 $(function () {
|
|
|
31 // create an instance when the DOM is ready
|
|
|
32 $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
|
|
|
33 window.open( data.node.a_attr.href, data.node.a_attr.target )
|
|
|
34 });
|
|
|
35 });
|
|
|
36 </script>
|
|
|
37
|
|
|
38 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
|
|
|
39 knitr::opts_chunk$set(echo = TRUE, error = TRUE)
|
|
|
40 ```
|
|
|
41
|
|
|
42
|
|
|
43
|
|
|
44
|
|
|
45
|
|
|
46
|
|
|
47
|
|
|
48
|
|
|
49
|
|
|
50
|
|
|
51
|
|
|
52
|
|
|
53
|
|
|
54
|
|
|
55
|
|
|
56
|
|
|
57
|
|
|
58
|
|
|
59
|
|
|
60
|
|
|
61
|
|
|
62 # Output
|
|
|
63
|
|
|
64 ```{bash, echo=FALSE}
|
|
|
65 # copy jstree directory to output directory
|
|
|
66 cp -r ${X_t}/vakata-jstree-3.3.5 ${X_d}
|
|
|
67 ```
|
|
|
68
|
|
|
69 ```{r, echo=FALSE}
|
|
|
70 # get the OUTPUT_DIR folder data: dataset_NUMBER_files
|
|
|
71 output_dir = tail(strsplit(opt$X_d, '/')[[1]], 1)
|
|
|
72 # define a recursive function to build html string of the file tree
|
|
|
73 file_tree = function(dir = '.'){
|
|
|
74 files = list.files(path = dir, recursive = FALSE, full.names = TRUE)
|
|
|
75 # files also include directorys, need to remove directorys
|
|
|
76 files = files[!dir.exists(files)]
|
|
|
77 dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE)
|
|
|
78 tags$ul(
|
|
|
79 {
|
|
|
80 if (length(files) > 0) {
|
|
|
81 lapply(files, function(x){
|
|
|
82 path_end = tail(strsplit(x, '/')[[1]],1)
|
|
|
83 href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
|
|
|
84 li_item = tags$li(tags$a(path_end, href=href_path))
|
|
|
85 li_item$attribs = list('data-jstree'='{"icon":"jstree-file"}')
|
|
|
86 li_item
|
|
|
87 })
|
|
|
88 }
|
|
|
89 },
|
|
|
90 {
|
|
|
91 if (length(dirs) > 0) {
|
|
|
92 lapply(dirs, function(x){
|
|
|
93 x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
|
|
|
94 li_item = tags$li(x_path, file_tree(x))
|
|
|
95 li_item$attribs = list('data-jstree'='{"icon":"jstree-folder"}')
|
|
|
96 li_item
|
|
|
97 })
|
|
|
98 }
|
|
|
99 }
|
|
|
100 )
|
|
|
101 }
|
|
|
102 ```
|
|
|
103
|
|
|
104 ```{r, echo=FALSE}
|
|
|
105 # create a div container to store the file tree interface
|
|
|
106 tags$div(
|
|
|
107 id="jstree",
|
|
|
108 file_tree(opt$X_d)
|
|
|
109 )
|
|
|
110 ```
|
|
|
111
|
