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annotate rmarkdown_report.Rmd @ 2:e08dd15646c6 draft

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planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
author mingchen0919
date Thu, 13 Dec 2018 23:45:31 -0500
parents 803f4888f36a
children
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1 ---
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2 title: 'HTSeq-count Report'
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3 output:
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4 html_document:
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5 highlight: pygments
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6 ---
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7
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8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
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10 ```
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12 ```{css, echo=FALSE}
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13 pre code, pre, code {
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14 white-space: pre !important;
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15 overflow-x: scroll !important;
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16 word-break: keep-all !important;
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17 word-wrap: initial !important;
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18 }
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19 ```
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21 ```{r, echo=FALSE}
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22 # to make the css theme to work, <link></link> tags cannot be added directly
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23 # as <script></script> tags as below.
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24 # it has to be added using a code chunk with the htmltool functions!!!
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25 css_link = tags$link()
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26 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
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27 css_link
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28 ```
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30 ```{r, eval=FALSE, echo=FALSE}
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31 # this code chunk is purely for adding comments
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32 # below is to add jQuery and jstree javascripts
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33 ```
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35 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
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38 ```{r, eval=FALSE, echo=FALSE}
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39 # this code chunk is purely for adding comments
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40 # javascript code below is to build the file tree interface
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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
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42 ```
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43 <script>
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44 jQuery(function () {
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45 // create an instance when the DOM is ready
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46 jQuery('#jstree').jstree().bind("select_node.jstree", function (e, data) {
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47 window.open( data.node.a_attr.href, data.node.a_attr.target )
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48 });
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49 });
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50 </script>
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51
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52
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53 ```{r, eval=FALSE, echo=FALSE}
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54 ---
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55 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
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56 ---
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57 ```
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59 ## Job script
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60
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61 ```{bash, echo=FALSE}
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62 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
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63 ```
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64
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65 ```{r echo=FALSE, comment='', results='asis'}
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66 cat('```bash\n')
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67 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
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68 cat('\n```')
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69 ```
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70
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71 ## Counts
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72
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73 Write data into a CSV file.
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74
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75 ```{r, echo=TRUE}
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76 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
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77 sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
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78 colnames(count_data) = rep(sample_names, length = ncol(count_data))
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81 # modify column names
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82 count_data = data.frame(feature_id = rownames(count_data), count_data)
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83 write.csv(count_data,
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84 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
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85 quote = FALSE, row.names = FALSE)
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86 ```
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87
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88 Display the top 1000 rows with largest average counts.
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89
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90 ```{r echo=TRUE}
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91 # Sort count table by count average
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92 rownames(count_data) = count_data$feature_id
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93 count_data = count_data[, -1]
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94 sorted_ct_table = count_data[order(rowMeans(count_data), decreasing = TRUE), ]
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95 DT::datatable(head(sorted_ct_table, 1000))
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96 ```
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