<%@meta language="R-vignette" content="--------------------------------
DIRECTIVES FOR R:
%\VignetteIndexEntry{RSP: A Brief Introduction}
%\VignetteAuthor{Henrik Bengtsson}
%\VignetteKeyword{R}
%\VignetteKeyword{RSP markup language}
%\VignetteKeyword{literate programming}
%\VignetteKeyword{reproducible research}
%\VignetteKeyword{report generator}
%\VignetteKeyword{Sweave}
%\VignetteKeyword{knitr}
%\VignetteKeyword{brew}
%\VignetteKeyword{noweb}
%\VignetteKeyword{TeX}
%\VignetteKeyword{LaTeX}
%\VignetteKeyword{Markdown}
%\VignetteKeyword{AsciiDoc}
%\VignetteKeyword{reStructuredText}
%\VignetteKeyword{Org-Mode}
%\VignetteKeyword{HTML}
%\VignetteKeyword{PDF}
%\VignetteEngine{R.rsp::rsp}
%\VignetteTangle{FALSE}
--------------------------------------------------------------------"%>
<% t0 <- Sys.time() %>
<%---------------------------------------------------------------------
Usage:
html <- R.rsp::rfile("RSP_intro.html.rsp")
---------------------------------------------------------------------%>
<%@string version="${rsp_version}" default="release"%>
<%---------------------------------------------------------------------
SETUP
---------------------------------------------------------------------%>
<%
R.utils::use("R.devices")
options("devEval/args/field" = "dataURI")
devOptions("png", width = 840)
%>
<%---------------------------------------------------------------------
RSP TEMPLATES
---------------------------------------------------------------------%>
<% page <- 2L; maxSlide <- 15L; %>
<% slide <- function(title) { %>
---
# <%= title %>
<% } # slide() %>
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title><%@meta name="title"%></title>
<meta name="author" content="<%@meta name="author"%>">
<meta name="keywords" content="<%@meta name="keywords"%>">
<style>
body {
font-family: serif;
}
h1, h2, h3 {
font-family: sans-serif;
font-weight: normal;
}
section {
font-size: 16pt;
}
h1 {
-webkit-margin-before: 0.27em;
-webkit-margin-after: 0.67em;
}
ul {
padding-left: 2ex;
list-style-position: outside;
}
li {
margin-top: 0.75ex;
}
.remark-slide-content h1 { font-size: 140%; }
.remark-slide-content h2 { font-size: 100%; }
.remark-slide-content h3 { font-size: 90%; }
.remark-slide-content {
font-size: 115%;
/* Defaults: 1em 4em 1em 4em; */
margin: 0ex;
padding: 0em 3em 0em 3em;
}
.remark-code, .remark-inline-code {
font-family: monospace;
font-weight: bold;
font-size: 90%;
}
img.screenshot-center {
position: relative;
bottom: 20%;
width: 100%;
box-shadow: 10px 10px 5px #888888;
}
img.screenshot-center-medium {
position: relative;
bottom: 20%;
width: 70%;
box-shadow: 10px 10px 5px #888888;
}
th {
background-color: #f2f2f2;
}
tr:nth-child(even) {
background-color: #f2f2f2
}
.blank {
background-color: white;
}
td {
width: 20%;
}
td:first-child {
width: 15%;
}
#author {
font-size: 150%;
}
.footnote-large {
position: absolute;
bottom: 3%;
font-size: 120%;
}
.footnote-small {
position: absolute;
bottom: 5%;
font-size: 80%;
}
</style>
</head>
<body>
<textarea id="source" style="visibility: hidden">
# <%@meta name="title"%>
by <%@meta name="author"%>, <%=format(as.Date(R.rsp$date), format="%Y-%m-%d")%>
Available on <a href="https://cran.r-project.org/package=R.rsp">CRAN</a> since 2005 (first version ~2002):
```r
install.packages("R.rsp")
```
```r
> library("R.rsp")
> rcat("A random number: <%%= sample(1:10, size = 1) %%>")
A random number: 7
```
<%---------------------------------------------------------------------%>
<% slide("Objectives") %>
<%---------------------------------------------------------------------%>
* Dynamically generate documents and reports (and web/help pages).
* Quickly turn your favorite static report template into a dynamic one.
* Support _all_ formats, e.g. LaTeX, Markdown, HTML, ...
<%-- * Support multiple languages, e.g. R, bash, ... --%>
* Supplement and/or complement Sweave, knitr, ...
* Mix and match code and text however you want.
* Simplify sharing of template and output documents.
* Use for R package vignettes.
## Some usage
* PSCBS: PDF reports of copy-number segmentation results
* aroma-project.org: Interactive [Chromosome Explorer](http://aroma-project.org/data/reports/GSE8605/ACC,-XY,BPN,-XY,AVG,FLN,-XY,paired/ChromosomeExplorer.html) and [Array Explorer](http://www.aroma-project.org/data/reports/GSE8605/raw/ArrayExplorer.html)
<%---------------------------------------------------------------------%>
<% slide("Compiling RSP document into PDF, HTML, ...")%>
<%---------------------------------------------------------------------%>
```r
> rfile("http://example.org/vignette.tex.rsp")
RspFileProduct:
Pathname: vignette.pdf
File size: 258.71 kB (264925 bytes)
Content type: application/pdf
Metadata 'title': 'Dynamic document creation using RSP'
Metadata 'keywords': 'Literate programming, HTML, PDF'
Metadata 'author': 'Henrik Bengtsson'
```
<%---------------------------------------------------------------------%>
<% slide("Very simple idea: Translate RSP to R and evaluate")%>
<%---------------------------------------------------------------------%>
## 1. RSP document
```
Title: Example
Counting:<%% for (i in 1:3) { %%>
<%%= i %%>
<%% } %%>
```
## 2. R script
```r
cat("Title: Example\nCounting:")
for (i in 1:3) {
cat(" ")
cat(i)
}
```
## 3. RSP output
```
Title: Example
Counting: 1 2 3
```
<%---------------------------------------------------------------------%>
<% slide("RSP Markup Language")%>
<%---------------------------------------------------------------------%>
## 1. RSP comments (`<%%-- ... --%%>`)
## 2. RSP preprocessing directives (`<%%@ ... %%>`)
## 3. RSP code expressions (`<%% ... %%>`)
<%---------------------------------------------------------------------%>
<% slide("RSP Markup Language")%>
<%---------------------------------------------------------------------%>
## 1. RSP comments (`<%%-- ... --%%>`)
```
<%%-----------------------------
Compile to PDF:
R.rsp::rfile("report.tex.rsp")
------------------------------%%>
\documentclass{report}
...
```
RSP comments drop anything within, e.g. private notes, other RSP constructor (nested comments too) and will never be part of the output.
<%---------------------------------------------------------------------%>
<% slide("RSP Markup Language")%>
<%---------------------------------------------------------------------%>
## 2. RSP preprocessing directives (`<%%@ ... %%>`)
### Including local and online files
```
<%%@include file="http://example.org/QC.tex.rsp"%%>
```
### Conditional inclusion
```
<%%@ifeq version="devel"%%>
<%%@include file="templates/QA-devel.tex.rsp"%%>
<%%@else%%>
Quality assessment is still under development.
<%%@endif%%>
```
### Meta data
```
<%%@meta title="Example"%%>
\hypersetup{pdftitle=<%%@meta name="title"%%>}
\title{<%%@meta name="title"%%>}
```
RSP preprocessing directives are independent of R, i.e. they would look the same with RSP for Python.
<%---------------------------------------------------------------------%>
<% slide("RSP Markup Language")%>
<%---------------------------------------------------------------------%>
## 3. RSP code expressions (`<%% ... %%>`)
### Insert value of evaluated R expressions
```
<%%= sample(1:100, size = 1) %%>
```
<br>
### Code snippets - mixture of RSP and text
```
<%% for (i in 1:3) { %%>
Step <%%= i %%>.
<%% } %%>
```
<%---------------------------------------------------------------------%>
<% slide("Looping over mixtures of code and text")%>
<%---------------------------------------------------------------------%>
```
<%% fit <- segmentByPairedPSCBS(data) %%>
\section{Segmentation results}
<%% for (chr in 1:23) { %%>
\subsection{Chromosome <%%= chr %%>}
<%% fitT <- extractChromosome(fit, chr) %%>
PSCBS identified <%%= nbrOfSegments(fitT) %%> segments
on Chr. <%%= chr %%>.
...
<%% } # for (chr ...) %%>
```
<br>
To achieve the same using noweb-style markup (e.g. Sweave and knitr) is tedious.
<%---------------------------------------------------------------------%>
<% slide("RSP template functions")%>
<%---------------------------------------------------------------------%>
```
<%%-- RSP TEMPLATES --%%>
<%% chromosomeSummary <- function(chr) { %%>
<%% fitT <- extractChromosome(fit, chr) %%>
PSCBS identified <%%= nbrOfSegments(fitT) %%> segments
on Chr. <%%= chr %%>.
...
<%% } %%>
<%%-- DOCUMENT --%%>
...
<%% for (chr in 1:23) { %%>
\subsection{Chromosome <%%= chr %%>}
<%% chromosomeSummary(chr) %%>
<%% } # for (chr ...) %%>
```
<%---
<%---------------------------------------------------------------------%>
<% slide("RSP template functions")%>
<%---------------------------------------------------------------------%>
```
<%%-- RSP TEMPLATES --%%>
<%%@include file="http://example.org/chrSum.tex.rsp"%%>
<%%-- DOCUMENT --%%>
...
<%% for (chr in 1:23) { %%>
\subsection{Chromosome <%%=chr%%>}
<%% chromosomeSummary(chr) %%>
<%% } # for (chr ...) %%>
```
---%>
<%---------------------------------------------------------------------%>
<% slide("R.rsp package - RSP engine for R")%>
<%---------------------------------------------------------------------%>
## rcat() - RSP version of cat()
```r
> rcat("A random integer in [1,100]:
<%%=sample(1:100, size = 1)%%>\n")
A random integer in [1,100]: 77
```
<br>
## rsource() - RSP version of source()
Consider RSP file 'count.rsp' (think 'count.R'):
```
Counting:<%% for (i in 1:10) { %%>
<%% Sys.sleep(0.3) %%><%%= i %%>
<%% } %%>.
```
Running this RSP script gives:
```r
> rsource("count.rsp")
Counting: 1 2 3 4 5 6 7 8 9 10.
```
<%---------------------------------------------------------------------%>
<% slide("rfile() - end-to-end compilation")%>
<%---------------------------------------------------------------------%>
```r
> rfile("report.md.rsp", args = list(n = 50, model = "L1"))
RspFileProduct:
Pathname: report.html
File size: 42.54 kB (43564 bytes)
Content type: text/html
```
<br>
```r
> rfile("http://example.org/vignette.tex.rsp")
RspFileProduct:
Pathname: vignette.pdf
File size: 258.71 kB (264925 bytes)
Content type: application/pdf
Metadata 'title': 'Dynamic document creation using RSP'
Metadata 'keywords': 'Literate programming, HTML, PDF'
Metadata 'author': 'Henrik Bengtsson'
```
<%---------------------------------------------------------------------%>
<% slide("Including graphics (R.devices package)") %>
<%---------------------------------------------------------------------%>
RSP-embedded LaTeX
```
\includegraphics{<%%= toPDF("MyFigure,yeah,cool", {
curve(dnorm, from = -5, to = +5)
}) %%>}
```
generates the image file and outputs
```
\includegraphics{MyFigure,yeah,cool}
```
which appears as
<img src="<%= toPNG("MyFigure,yeah,cool", aspectRatio = 0.5, {
par(cex = 2, mar = c(4,3,1,1), mgp = c(1.8,0.5,0))
curve(dnorm, from = -5, to = +5);
})%>" width=480>
<%---------------------------------------------------------------------%>
<% slide("Appendix") %>
<%---------------------------------------------------------------------%>
Session info:
```
<% print(sessionInfo()) %>
```
These slides were generated using `R.rsp::rfile()` in <%= dt <- round(Sys.time()-t0, digits = 2) %> <%= attr(dt, "units") %>.
</textarea>
<script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
<script>
var slideshow = remark.create({
ratio: '4:3',
})
</script>
</body>
</html>