Mercurial > repos > mingchen0919 > aurora_skewer

annotate rmarkdown_report.Rmd @ 0:0358f6f78adf draft

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author mingchen0919
date Fri, 14 Dec 2018 00:40:15 -0500
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1 ---
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2 title: 'Aurora Skewer 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$set(error = TRUE, echo = FALSE)
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10 ```
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11
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12 ```{css, echo=FALSE}
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13 pre code, pre, code {
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14 white-space: pre !important;
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15 overflow-x: scroll !important;
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16 word-break: keep-all !important;
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17 word-wrap: initial !important;
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18 }
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19 ```
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20
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21 ```{r, echo=FALSE}
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22 # to make the css theme to work, <link></link> tags cannot be added directly
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23 # as <script></script> tags as below.
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24 # it has to be added using a code chunk with the htmltool functions!!!
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25 css_link = tags$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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29
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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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34
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35 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
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37
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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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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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58
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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
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63 ```
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64
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65 ```{r echo=FALSE,warning=FALSE,results='asis'}
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66 # display content of the job-script.sh file.
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67 cat('```bash\n')
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68 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/job-1-script.sh')), sep = '\n')
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69 cat('\n```')
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70 ```
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71
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72 # Results summary
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73
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74 ## Reads processing summary
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75
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76 ```{r echo=TRUE}
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77 log = readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/trim-trimmed.log'))
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78 start_line = grep('read.+processed; of these:', log)
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79 end_line = grep('untrimmed.+available after processing', log)
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80 processing_summary = gsub('(\\d+) ', '\\1\t', log[start_line:end_line])
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81 processing_summary_df = do.call(rbind, strsplit(processing_summary, '\t'))
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82 colnames(processing_summary_df) = c('Total reads:', processing_summary_df[1,1])
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83 knitr::kable(processing_summary_df[-1, ])
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84 ```
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85
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86 ## Length distribution of reads after trimming
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87
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88 ```{r echo=TRUE, message=FALSE, warning=FALSE}
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89 start_line = grep('length count percentage', log)
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90 len_dist = log[(start_line):length(log)]
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91 len_dist = do.call(rbind, strsplit(len_dist, '\t'))
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92 columns = len_dist[1, ]
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93 len_dist = as.data.frame(len_dist[-1, ])
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94 colnames(len_dist) = columns
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95
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96 library(plotly)
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97 library(ggplot2)
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98 len_dist$count = as.numeric(len_dist$count)
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99 labels = as.character(len_dist$length)
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100 len_dist$length = 1:nrow(len_dist)
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101 pp = ggplot(data = len_dist, aes(length, count)) +
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102 geom_line(color='red') +
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103 scale_x_continuous(name = 'Length',
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104 breaks = 1:nrow(len_dist),
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105 labels = labels) +
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106 theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
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107 ylab('Count') +
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108 ggtitle('Length distribution')
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109 ggplotly(pp)
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110 ```
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111