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Observation: The spinner and the loading message text seems to block the actual RMD text sometimes and is distracting. (check the attached snapshot). Though this is not a major issue thats affecting any functionality, is there a way to hide the text if at all possible?
Rmd example:
My First R Markdown Document using bslib
```` --- title: "My First R Markdown Document" author: "Author: Your Name" date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" runtime: shiny output: html_document: theme: !expr bslib::bs_theme() toc: true toc_float: collapsed: true smooth_scroll: true toc_depth: 3 fig_caption: yes code_folding: show code_download: true number_sections: true --- ```{r, echo = FALSE} thematic::thematic_shiny(font = "auto") bslib::bs_themer() ``` # R Markdown ## Overview R Markdown combines markdown (an easy to write plain text format) with embedded R code chunks. When compiling R Markdown documents, the code components can be evaluated so that both the code and its output can be included in the final document. This makes analysis reports highly reproducible by allowing to automatically regenerate them when the underlying R code or data changes. R Markdown documents (`.Rmd` files) can be rendered to various formats including HTML and PDF. The R code in an `.Rmd` document is processed by `knitr`, while the resulting `.md` file is rendered by `pandoc` to the final output formats (_e.g._ HTML or PDF). Historically, R Markdown is an extension of the older `Sweave/Latex` environment. Rendering of mathematical expressions and reference management is also supported by R Markdown using embedded Latex syntax and Bibtex, respectively. ## Quick Start ### Install R Markdown ```{r install_rmarkdown, eval=FALSE} install.packages("rmarkdown") ``` ### Initialize a new R Markdown (`Rmd`) script To minimize typing, it can be helful to start with an R Markdown template and then modify it as needed. Note the file name of an R Markdown scirpt needs to have the extension `.Rmd`. Template files for the following examples are available here: + R Markdown sample script: [`sample.Rmd`](https://raw.githubusercontent.com/tgirke/GEN242/gh-pages/_vignettes/07_Rbasics/sample.Rmd) + Bibtex file for handling citations and reference section: [`bibtex.bib`](https://raw.githubusercontent.com/tgirke/GEN242/gh-pages/_vignettes/07_Rbasics/bibtex.bib) Users want to download these files, open the `sample.Rmd` file with their preferred R IDE (_e.g._ RStudio, vim or emacs), initilize an R session and then direct their R session to the location of these two files. ### Metadata section The metadata section (YAML header) in an R Markdown script defines how it will be processed and rendered. The metadata section also includes both title, author, and date information as well as options for customizing the output format. For instance, PDF and HTML output can be defined with `pdf_document` and `html_document`, respectively. The `BiocStyle::` prefix will use the formatting style of the [`BiocStyle`](http://bioconductor.org/packages/release/bioc/html/BiocStyle.html) package from Bioconductor. ``` --- title: "My First R Markdown Document" author: "Author: First Last" date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" output: BiocStyle::html_document: toc: true toc_depth: 3 fig_caption: yes fontsize: 14pt bibliography: bibtex.bib --- ``` ### Render `Rmd` script An R Markdown script can be evaluated and rendered with the following `render` command or by pressing the `knit` button in RStudio. The `output_format` argument defines the format of the output (_e.g._ `html_document`). The setting `output_format="all"` will generate all supported output formats. Alternatively, one can specify several output formats in the metadata section as shown in the above example. ```{r render_rmarkdown, eval=FALSE, message=FALSE} rmarkdown::render("sample.Rmd", clean=TRUE, output_format="html_document") ``` The following shows two options how to run the rendering from the command-line. ```{sh render_commandline, eval=FALSE, message=FALSE} $ Rscript -e "rmarkdown::render('sample.Rmd', clean=TRUE)" ``` Alternatively, one can use a Makefile to evaluate and render an R Markdown script. A sample Makefile for rendering the above `sample.Rmd` can be downloaded [`here`](https://raw.githubusercontent.com/tgirke/GEN242/gh-pages/_vignettes/07_Rbasics/Makefile). To apply it to a custom `Rmd` file, one needs open the Makefile in a text editor and change the value assigned to `MAIN` (line 13) to the base name of the corresponding `.Rmd` file (_e.g._ assign `systemPipeRNAseq` if the file name is `systemPipeRNAseq.Rmd`). To execute the `Makefile`, run the following command from the command-line. ```{sh render_makefile, eval=FALSE, message=FALSE} $ make -B ``` ### R code chunks R Code Chunks can be embedded in an R Markdown script by using three backticks at the beginning of a new line along with arguments enclosed in curly braces controlling the behavior of the code. The following lines contain the plain R code. A code chunk is terminated by a new line starting with three backticks. The following shows an example of such a code chunk. Note the backslashes are not part of it. They have been added to print the code chunk syntax in this document. ``` ```\{r code_chunk_name, eval=FALSE\} x <- 1:10 ``` ``` The following lists the most important arguments to control the behavior of R code chunks: + `r`: specifies language for code chunk, here R + `chode_chunk_name`: name of code chunk; this name needs to be unique + `eval`: if assigned `TRUE` the code will be evaluated + `warning`: if assigned `FALSE` warnings will not be shown + `message`: if assigned `FALSE` messages will not be shown + `cache`: if assigned `TRUE` results will be cached to reuse in future rendering instances + `fig.height`: allows to specify height of figures in inches + `fig.width`: allows to specify width of figures in inches For more details on code chunk options see [here](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf). ### Learning Markdown The basic syntax of Markdown and derivatives like kramdown is extremely easy to learn. Rather than providing another introduction on this topic, here are some useful sites for learning Markdown: + [Markdown Intro on GitHub](https://guides.github.com/features/mastering-markdown/) + [Markdown Cheet Sheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) + [Markdown Basics from RStudio](http://rmarkdown.rstudio.com/authoring_basics.html) + [R Markdown Cheat Sheet](http://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf) + [kramdown Syntax](http://kramdown.gettalong.org/syntax.html) ### Tables There are several ways to render tables. First, they can be printed within the R code chunks. Second, much nicer formatted tables can be generated with the functions `kable`, `pander` or `xtable`. The following example uses `kable` from the `knitr` package. ```{r kable} library(knitr) kable(iris[1:12,]) ``` A much more elegant and powerful solution is to create fully interactive tables with the [`DT` package](https://rstudio.github.io/DT/). This JavaScirpt based environment provides a wrapper to the DataTables library using jQuery. The resulting tables can be sorted, queried and resized by the user. ```{r dt} library(DT) datatable(iris, filter = 'top', options = list( pageLength = 100, scrollX = TRUE, scrollY = "600px", autoWidth = TRUE )) ``` ### Figures Plots generated by the R code chunks in an R Markdown document can be automatically inserted in the output file. The size of the figure can be controlled with the `fig.height` and `fig.width` arguments. ```{r some_jitter_plot, warning=FALSE} library(ggplot2) renderPlot({ dsmall <- diamonds[sample(nrow(diamonds), 1000), ] ggplot(dsmall, aes(color, price/carat)) + geom_jitter(alpha = I(1 / 2), aes(color=color)) }) ``` ### Inline R code To evaluate R code inline, one can enclose an R expression with a single back-tick followed by `r` and then the actual expression. For instance, the back-ticked version of 'r 1 + 1' evaluates to `r 1 + 1` and 'r pi' evaluates to `r pi`. ### Mathematical equations To render mathematical equations, one can use standard Latex syntax. When expressions are enclosed with single `$` signs then they will be shown inline, while enclosing them with double `$$` signs will show them in display mode. For instance, the following Latex syntax `d(X,Y) = \sqrt[]{ \sum_{i=1}^{n}{(x_{i}-y_{i})^2} }` renders in display mode as follows: $$d(X,Y) = \sqrt[]{ \sum_{i=1}^{n}{(x_{i}-y_{i})^2} }$$ ````