Mercurial > repos > mingchen0919 > aurora_htseq
view htseq_count.Rmd @ 10:ec906e72784d draft
planemo upload commit e2f267840cded7ba17bb75a074796a4babbaab5b-dirty
author | mingchen0919 |
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date | Thu, 26 Apr 2018 12:24:33 -0400 |
parents | 578a96df8690 |
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--- title: 'htseq-count analysis report' output: html_document: highlight: pygments --- ```{css echo=FALSE} # code chunks scrollable pre code, pre, code { white-space: pre !important; overflow-x: scroll !important; word-break: keep-all !important; word-wrap: initial !important; } ``` ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_knit$set(progress = FALSE) knitr::opts_chunk$set(error = TRUE, echo = FALSE) ``` ```{r, echo=FALSE} # to make the css theme to work, <link></link> tags cannot be added directly # as <script></script> tags as below. # it has to be added using a code chunk with the htmltool functions!!! css_link = tags$link() css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css") css_link ``` ```{r, eval=FALSE, echo=FALSE} # this code chunk is purely for adding comments # below is to add jQuery and jstree javascripts ``` <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script> <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script> ```{r, eval=FALSE, echo=FALSE} # this code chunk is purely for adding comments # javascript code below is to build the file tree interface # 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 ``` <script> $(function () { // create an instance when the DOM is ready $('#jstree').jstree().bind("select_node.jstree", function (e, data) { window.open( data.node.a_attr.href, data.node.a_attr.target ) }); }); </script> ----------------------------------------- ## Job script ```{bash, echo=FALSE} sh ${TOOL_INSTALL_DIR}/shell-script-template.sh ``` ```{r echo=FALSE, comment='', results='asis'} cat('```bash\n') cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n') cat('\n```') ``` ## Counts Only the first few rows are displayed. ```{r, echo=FALSE} count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1) sample_names = trimws(strsplit(opt$X_B, ',')[[1]]) colnames(count_data) = rep(sample_names, length = ncol(count_data)) kable(head(count_data)) # modify column names count_data = data.frame(feature_id = rownames(count_data), count_data) write.csv(count_data, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'), quote = FALSE, row.names = FALSE) ``` ----------------------------------------- ## Output ```{r, echo=FALSE} # create a div container to store the file tree interface tags$div( id="jstree", file_tree(Sys.getenv('REPORT_FILES_PATH')) ) ```