CircosHeatmap-aardio/dist/lib/r-library/knitr/examples/knitr-themes.lyx

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\pdf_author "Ramnath Vaidyanathan"
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<<setup, include=FALSE, cache=FALSE>>=
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library(knitr)
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opts_chunk$set(fig.path='figure/theme-', cache.path='cache/theme-', cache=TRUE)
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options(formatR.arrow=TRUE,width=78)
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knit_hooks$set(par=function(before, options, envir){if (before) par(mar=c(4,4,.1,.
1),cex.lab=.95,cex.axis=.9,mgp=c(2,.7,0),tcl=-.3)})
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@
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<<solarized-theme, cache=FALSE, echo=FALSE>>=
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\begin_layout Plain Layout

thm = knit_theme$get("solarized-dark")
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knit_theme$set(thm)
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@
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\end_layout

\begin_layout Title
Customizing Syntax Highlighting Themes
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\begin_layout Author
Yihui Xie & Ramnath Vaidyanathan
\end_layout

\begin_layout Abstract
This manual
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source code at 
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status collapsed

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https://github.com/yihui/knitr/blob/master/inst/examples/knitr-themes.Rnw
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 shows how to customize syntax highlighting of source code using themes.
 It walks the user through the basics of syntax highlighting in 
\series bold
knitr
\series default
, and the use of built-in themes.
\end_layout

\begin_layout Standard
The 
\series bold
knitr
\series default
 package uses the 
\series bold
highr
\series default
 package to highlight source code in a document.
 In short, the 
\series bold
highr
\series default
 package parses the source code, tokenizes it into grammar symbols, and
 formats their appearance using CSS or LaTeX commands.
 
\end_layout

\begin_layout Section
Usage
\end_layout

\begin_layout Standard
We can use the object 
\family typewriter
knit_theme
\family default
 to set / get a theme.
 See 
\family typewriter
?knit_theme
\family default
 for the usage.
 For example, we set the theme of this document to be 
\family typewriter
solarized-dark
\family default
:
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status open

\begin_layout Plain Layout

<<solarized-theme>>=
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\begin_layout Plain Layout

@
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\begin_layout Section
Built-in Themes
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wide false
sideways false
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<<eclipse-css, comment=NA, echo=FALSE>>=
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cat(c(readLines('../themes/edit-eclipse.css', n=30),'...'),sep='
\backslash
n')
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@
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\begin_layout Standard
The listing on the right shows the CSS file for one of the themes, 
\family typewriter
edit-eclipse
\family default
, which was adapted from Andre Simon's excellent highlighter
\begin_inset Foot
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http://www.andre-simon.de/
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.
 The 
\series bold
knitr
\series default
 package comes pre-loaded with a number of themes based on this highlighter.
 Here is list of all available code themes
\begin_inset Foot
status open

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For a preview of all themes, see 
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https://gist.github.com/yihui/3422133
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:
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<<all-themes>>=
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\begin_layout Plain Layout

knit_theme$get()
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\begin_layout Plain Layout

@
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\end_inset


\end_layout

\begin_layout Standard
Shown below is how the 
\family typewriter
solarized-dark
\family default
 theme looks like when applied to R code:
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\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<demo-code, eval = FALSE>>=
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\begin_layout Plain Layout

library(XML)
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\begin_layout Plain Layout

library(plyr)
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\begin_layout Plain Layout

library(reshape)
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\begin_layout Plain Layout

# SCRAPE THE DATA FROM WEB 
\end_layout

\begin_layout Plain Layout

\end_layout

\begin_layout Plain Layout

base_url = "http://www.mlsoccer.com/stats/%s/reg"
\end_layout

\begin_layout Plain Layout

years    = 1996:2010
\end_layout

\begin_layout Plain Layout

options(width = 40)
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\begin_layout Plain Layout

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\begin_layout Plain Layout

#' Function to save data for each year
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save_data = function(y){
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  url  = sprintf(base_url, y)
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  tab  = readHTMLTable(url, header = FALSE, stringsAsFactors = FALSE);
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  pos  = max(grep("United", tab));
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  tab  = tab[[pos]];
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  tab$year   = y;
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  return(tab)            
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}
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team.list  = llply(years, save_data);
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mls        = merge_recurse(team.list);
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@
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\begin_layout Section
Misc
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\begin_layout Standard
One thing to consider is the foreground color of plots when we use dark
 themes; we need to make it lighter, otherwise the graphical elements will
 be difficult to be read.
 We can access the foreground color of the theme in the list returned by
 
\family typewriter
knit_theme$get(theme)
\family default
, e.g., for this document:
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<<fg-color>>=
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## the object thm is from the first chunk
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thm$foreground  # foreground color
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thm$background  # background color
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@
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When we make plots, we may use these colors, e.g.
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<<plot-color, fig.width=6, fig.height=4, out.width='.8
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\backslash
linewidth', par=TRUE>>=
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## can design a chunk hook to set foreground color automatically
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fgcolor=thm$foreground
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par(fg=fgcolor, col.axis=fgcolor, col.lab=fgcolor)
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plot(rnorm(100),pch=19)
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@
\end_layout

\end_inset


\end_layout

\begin_layout Standard
Of course, we do not need to worry about these colors when we use a white
 background for the plots.
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