Mercurial > repos > mingchen0919 > aurora_htseq
comparison htseq_count.Rmd @ 5:aacd5f53ac99 draft
v2.0.0
author | mingchen0919 |
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date | Wed, 18 Apr 2018 13:17:28 -0400 |
parents | 0fdb0d5f53ce |
children | 7c54fd452b8e |
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4:0fdb0d5f53ce | 5:aacd5f53ac99 |
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1 --- | 1 --- |
2 title: 'htseq-count analysis' | 2 title: 'htseq-count analysis' |
3 output: html_document | 3 output: |
4 html_document: | |
5 highlight: pygments | |
4 --- | 6 --- |
5 | 7 |
6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | 8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} |
7 knitr::opts_chunk$set( | 9 knitr::opts_knit$set(progress = FALSE) |
8 echo = as.logical(opt$X_e), | 10 knitr::opts_chunk$set(error = TRUE, echo = FALSE) |
9 error = TRUE | |
10 ) | |
11 ``` | 11 ``` |
12 | 12 |
13 | 13 ```{r, echo=FALSE} |
14 ## Run htseq-count | 14 # to make the css theme to work, <link></link> tags cannot be added directly |
15 | 15 # as <script></script> tags as below. |
16 ```{bash} | 16 # it has to be added using a code chunk with the htmltool functions!!! |
17 cd ${X_d} | 17 css_link = tags$link() |
18 | 18 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css") |
19 cat >htseq-count.sh <<EOF | 19 css_link |
20 htseq-count \\ | |
21 $(echo ${X_A} | sed 's/,/ /g') \\ | |
22 ${X_G} \\ | |
23 -f ${X_f} \\ | |
24 -r ${X_r} \\ | |
25 -s ${X_S} \\ | |
26 -a ${X_a} \\ | |
27 -t ${X_T} \\ | |
28 -i ${X_i} \\ | |
29 -m ${X_m} > counts.txt | |
30 | |
31 grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' counts.txt > ${X_c} | |
32 EOF | |
33 ``` | 20 ``` |
34 | 21 |
22 ```{r, eval=FALSE, echo=FALSE} | |
23 # this code chunk is purely for adding comments | |
24 # below is to add jQuery and jstree javascripts | |
25 ``` | |
26 <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script> | |
27 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script> | |
35 | 28 |
36 ```{r} | 29 ```{r, eval=FALSE, echo=FALSE} |
37 # display htseq-count job script | 30 # this code chunk is purely for adding comments |
38 htseq_count_sh = paste0(opt$X_d, '/htseq-count.sh') | 31 # javascript code below is to build the file tree interface |
39 tags$code(tags$pre(readChar(htseq_count_sh, file.info(htseq_count_sh)$size ))) | 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 $(function () { | |
36 // create an instance when the DOM is ready | |
37 $('#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> | |
42 ----------------------------------------- | |
43 | |
44 | |
45 ```{bash, echo=FALSE} | |
46 sh ${TOOL_INSTALL_DIR}/run_htseq-count.sh | |
40 ``` | 47 ``` |
41 | 48 |
42 ```{bash} | 49 ## Job script |
43 cd ${X_d} | 50 |
44 sh htseq-count.sh | 51 * htseq-count analysis: [htseq-count.sh](htseq-count.sh) |
45 ``` | |
46 | 52 |
47 ## Counts | 53 ## Counts |
48 | 54 |
49 ```{r} | 55 ```{r} |
50 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1) | 56 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1) |
60 | 66 |
61 ```{bash} | 67 ```{bash} |
62 cp ${X_d}/counts.RData ${X_O} | 68 cp ${X_d}/counts.RData ${X_O} |
63 ``` | 69 ``` |
64 | 70 |
71 ----------------------------------------- | |
72 ## Output | |
65 | 73 |
74 ```{r, echo=FALSE} | |
75 # create a div container to store the file tree interface | |
76 tags$div( | |
77 id="jstree", | |
78 file_tree(Sys.getenv('REPORT_FILES_PATH')) | |
79 ) | |
80 ``` |