Mercurial > repos > mingchen0919 > aurora_htseq

annotate rmarkdown_report.Rmd @ 3:6a3bbafa24b3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Fri, 14 Dec 2018 09:16:39 -0500
parents e08dd15646c6
children
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
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
12 ```{css, echo=FALSE}
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
13 pre code, pre, code {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
14 white-space: pre !important;
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
15 overflow-x: scroll !important;
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
16 word-break: keep-all !important;
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
17 word-wrap: initial !important;
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
18 }
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 ```{r, echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
22 # to make the css theme to work, <link></link> tags cannot be added directly
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
23 # as <script></script> tags as below.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
24 # it has to be added using a code chunk with the htmltool functions!!!
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
25 css_link = tags$link()
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
26 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
27 css_link
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
28 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
29
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
30 ```{r, eval=FALSE, echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
31 # this code chunk is purely for adding comments
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
32 # below is to add jQuery and jstree javascripts
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
33 ```
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
34
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
35 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
36
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
37
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
38 ```{r, eval=FALSE, echo=FALSE}
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
39 # this code chunk is purely for adding comments
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
40 # javascript code below is to build the file tree interface
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
41 # 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
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
42 ```
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
43 <script>
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
44 jQuery(function () {
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
45 // create an instance when the DOM is ready
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
46 jQuery('#jstree').jstree().bind("select_node.jstree", function (e, data) {
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
47 window.open( data.node.a_attr.href, data.node.a_attr.target )
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
48 });
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
49 });
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
50 </script>
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
51
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
52
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
53 ```{r, eval=FALSE, echo=FALSE}
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
54 ---
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
55 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
56 ---
2
e08dd15646c6 planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
mingchen0919
parents: 0
diff changeset
57 ```
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
58
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
59 ## Job script
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
60
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
61 ```{bash, echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
62 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
63 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
64
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
65 ```{r echo=FALSE, comment='', results='asis'}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
66 cat('```bash\n')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
67 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
68 cat('\n```')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
69 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
70
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
71 ## Counts
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
72
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
73 Write data into a CSV file.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
74
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
75 ```{r, echo=TRUE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
76 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
77 sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
78 colnames(count_data) = rep(sample_names, length = ncol(count_data))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
79
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
80
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
81 # modify column names
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
82 count_data = data.frame(feature_id = rownames(count_data), count_data)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
83 write.csv(count_data,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
84 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
85 quote = FALSE, row.names = FALSE)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
86 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
87
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
88 Display the top 1000 rows with largest average counts.
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 # Sort count table by count average
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
92 rownames(count_data) = count_data$feature_id
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
93 count_data = count_data[, -1]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
94 sorted_ct_table = count_data[order(rowMeans(count_data), decreasing = TRUE), ]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
95 DT::datatable(head(sorted_ct_table, 1000))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
96 ```
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
97
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
98