Mercurial > repos > mingchen0919 > aurora_htseq

annotate rmarkdown_report.Rmd @ 1:fd547674f29f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
author mingchen0919
date Thu, 13 Dec 2018 23:10:32 -0500
parents 803f4888f36a
children e08dd15646c6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
1 ---
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
2 title: 'HTSeq-count Report'
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
3 output:
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
4 html_document:
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
5 highlight: pygments
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
6 ---
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
7
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
10 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
11
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
12 ```{css echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
13 # code chunks scrollable
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
14 pre code, pre, code {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
15 white-space: pre !important;
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
16 overflow-x: scroll !important;
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
17 word-break: keep-all !important;
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
18 word-wrap: initial !important;
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
19 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
20 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
21
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
22
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
23 ```{r, echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
24 # to make the css theme to work, <link></link> tags cannot be added directly
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
25 # as <script></script> tags as below.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
26 # it has to be added using a code chunk with the htmltool functions!!!
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
27 css_link = tags$link()
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
28 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
29 css_link
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
30 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
31
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
32 ```{r, eval=FALSE, echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
33 # this code chunk is purely for adding comments
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
34 # below is to add jQuery and jstree javascripts
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
35 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
36 <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
37 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
38
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
39 ```{r, eval=FALSE, echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
40 # The script below is used to avoid conflicts between different javascript labraries
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
41 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
42
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
43 <script>
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
44 jQuery.noConflict();
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
45
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
46 jQuery( document ).ready(function( $ ) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
47 // You can use the locally-scoped $ in here as an alias to jQuery.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
48 $( "jstree" ).hide();
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
49 });
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
50
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
51 // The $ variable in the global scope has the prototype.js meaning.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
52 window.onload = function(){
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
53 var mainDiv = $( "main" );
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
54 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
55 </script>
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
56
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
57 ---
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
58 # javascript code below is to build the file tree interface
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
59 # 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
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
60 ---
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
61 <script>
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
62 $(function () {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
63 // create an instance when the DOM is ready
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
64 $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
65 window.open( data.node.a_attr.href, data.node.a_attr.target )
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
66 });
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
67 });
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
68 </script>
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
69
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
70 ---
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
71 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
72 ---
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
73
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
74 ## Job script
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
75
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
76 ```{bash, echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
77 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
78 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
79
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
80 ```{r echo=FALSE, comment='', results='asis'}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
81 cat('```bash\n')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
82 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
83 cat('\n```')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
84 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
85
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
86 ## Counts
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
87
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
88 Write data into a CSV file.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
89
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
90 ```{r, echo=TRUE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
91 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
92 sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
93 colnames(count_data) = rep(sample_names, length = ncol(count_data))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
94
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
95
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
96 # modify column names
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
97 count_data = data.frame(feature_id = rownames(count_data), count_data)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
98 write.csv(count_data,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
99 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
100 quote = FALSE, row.names = FALSE)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
101 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
102
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
103 Display the top 1000 rows with largest average counts.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
104
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
105 ```{r echo=TRUE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
106 # Sort count table by count average
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
107 rownames(count_data) = count_data$feature_id
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
108 count_data = count_data[, -1]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
109 sorted_ct_table = count_data[order(rowMeans(count_data), decreasing = TRUE), ]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
110 DT::datatable(head(sorted_ct_table, 1000))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
111 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
112
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
113