Mercurial > repos > mingchen0919 > aurora_htseq

annotate rmarkdown_report.Rmd @ 27:ada57b198dc1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit bb4923aaeb8563e3b8ecd44483f788b2992f9e98-dirty
author mingchen0919
date Sat, 01 Dec 2018 01:04:12 -0500
parents ad2ceb05d152
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
1 ---
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
2 title: 'HTSeq-count Report'
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
3 output:
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
4 html_document:
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
5 highlight: pygments
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
6 ---
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
7
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
10 ```
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
11
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
12 ```{css echo=FALSE}
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
13 # code chunks scrollable
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
14 pre code, pre, code {
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
15 white-space: pre !important;
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
16 overflow-x: scroll !important;
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
17 word-break: keep-all !important;
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
18 word-wrap: initial !important;
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
19 }
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
20 ```
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
21
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
22
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
23 ```{r, echo=FALSE}
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
24 # to make the css theme to work, <link></link> tags cannot be added directly
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
25 # as <script></script> tags as below.
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
26 # it has to be added using a code chunk with the htmltool functions!!!
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
27 css_link = tags$link()
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
28 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
29 css_link
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
30 ```
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
31
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
32 ```{r, eval=FALSE, echo=FALSE}
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
33 # this code chunk is purely for adding comments
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
34 # below is to add jQuery and jstree javascripts
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
35 ```
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
36 <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
37 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
38
21
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
39 ```{r, eval=FALSE, echo=FALSE}
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
40 # The script below is used to avoid conflicts between different javascript labraries
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
41 ```
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
42
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
43 <script>
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
44 jQuery.noConflict();
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
45
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
46 jQuery( document ).ready(function( $ ) {
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
47 // You can use the locally-scoped $ in here as an alias to jQuery.
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
48 $( "jstree" ).hide();
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
49 });
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
50
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
51 // The $ variable in the global scope has the prototype.js meaning.
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
52 window.onload = function(){
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
53 var mainDiv = $( "main" );
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
54 }
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
55 </script>
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
56
11
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
57 ---
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
58 # javascript code below is to build the file tree interface
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
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
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
60 ---
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
61 <script>
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
62 $(function () {
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
63 // create an instance when the DOM is ready
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
64 $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
65 window.open( data.node.a_attr.href, data.node.a_attr.target )
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
66 });
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
67 });
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
68 </script>
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
69
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
70 ---
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
71 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
72 ---
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
73
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
74 ## Job script
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
75
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
76 ```{bash, echo=FALSE}
14
851112a0071d planemo upload commit 8758ce271d51387da37298280356fb3f34c4db49-dirty
mingchen0919
parents: 11
diff changeset
77 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
11
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
78 ```
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
79
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
80 ```{r echo=FALSE, comment='', results='asis'}
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
81 cat('```bash\n')
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
82 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
83 cat('\n```')
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
84 ```
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
85
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
86 ## Counts
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
87
21
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
88 Write data into a CSV file.
11
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
89
21
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
90 ```{r, echo=TRUE}
11
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
91 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
92 sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
93 colnames(count_data) = rep(sample_names, length = ncol(count_data))
22
ad2ceb05d152 planemo upload commit 9d80f8019f1eb21b0bc6fdb4e3ae7684174f6ca4-dirty
mingchen0919
parents: 21
diff changeset
94
11
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
95
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
96 # modify column names
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
97 count_data = data.frame(feature_id = rownames(count_data), count_data)
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
98 write.csv(count_data,
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
99 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
100 quote = FALSE, row.names = FALSE)
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
101 ```
ce76fb2791e5 planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
102
21
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
103 Display the top 1000 rows with largest average counts.
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
104
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
105 ```{r echo=TRUE}
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
106 # Sort count table by count average
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
107 rownames(count_data) = count_data$feature_id
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
108 count_data = count_data[, -1]
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
109 sorted_ct_table = count_data[order(rowMeans(count_data), decreasing = TRUE), ]
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
110 DT::datatable(head(sorted_ct_table, 1000))
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
111 ```
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
112
69157062629f planemo upload commit e37a78252b05a1a274a750e55a1a74693b7abc18-dirty
mingchen0919
parents: 14
diff changeset
113