1998 lines
31 KiB
Plaintext
1998 lines
31 KiB
Plaintext
#LyX 2.1 created this file. For more info see http://www.lyx.org/
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knitr
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<<setup, include=FALSE, cache=FALSE>>=
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library(knitr)
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options(formatR.arrow=TRUE,width=50)
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opts_chunk$set(fig.path='figure/graphics-', cache.path='cache/graphics-',
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fig.align='center', dev='tikz', fig.width=5, fig.height=5, fig.show='hold',
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cache=TRUE, par=TRUE)
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knit_hooks$set(par=function(before, options, envir){
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\end_layout
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\begin_layout Title
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knitr Graphics Manual
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\end_layout
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\begin_layout Author
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Yihui Xie
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\end_layout
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\begin_layout Abstract
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This manual shows features of graphics in the
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\series bold
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knitr
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\series default
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package (version
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\backslash
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Sexpr{packageVersion('knitr')}
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\end_layout
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\end_inset
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) in detail, including the graphical devices, plot recording, plot rearrangement
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, control of plot sizes, the tikz device, figure captions, animations and
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other types of plots such as
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\series bold
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rgl
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\series default
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or GGobi plots.
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\end_layout
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\begin_layout Standard
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Before reading this specific manual
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status open
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status collapsed
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http://bit.ly/knitr-graphics-src
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\end_inset
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(Rnw source)
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\end_inset
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, you must have finished the main manual
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http://bit.ly/knitr-main
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\end_layout
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\end_inset
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.
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\end_layout
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\begin_layout Section
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Graphical Devices
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\end_layout
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\begin_layout Standard
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The
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\series bold
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knitr
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\series default
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package comes with more than 20 built-in graphical devices, and you can
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specify them through the
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\family typewriter
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dev
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\family default
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option.
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This document uses the global option
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\family typewriter
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dev='tikz'
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\family default
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, i.e., the plots are recorded by the tikz device by default, but we can change
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the device locally.
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Since tikz will be used extensively throughout this manual and you will
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see plenty of tikz graphics later, now we first show a few other devices.
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<<test-plot, eval=FALSE>>=
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with(trees, symbols(Height, Volume, circles = Girth/16, inches = FALSE,
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bg = 'deeppink', fg = 'gray30'))
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<<pdf-dev, ref.label='test-plot', dev='pdf', out.width='
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The default PDF device.
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@
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\begin_layout Plain Layout
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\begin_inset Caption Standard
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\begin_layout Plain Layout
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The PNG device.
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\begin_inset CommandInset label
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LatexCommand label
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name "mar:png-dev"
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\begin_layout Standard
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Figure
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\begin_inset CommandInset ref
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LatexCommand ref
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reference "mar:pdf-dev"
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\end_inset
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and
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\begin_inset CommandInset ref
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LatexCommand ref
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reference "mar:png-dev"
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\end_inset
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show two standard devices in the
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\series bold
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grDevices
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\series default
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package.
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We can also use devices in the
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\series bold
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Cairo
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\series default
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or
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\series bold
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cairoDevice
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\series default
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package, e.g., the chunk below uses the
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\emph on
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CairoPNG()
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\emph default
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device in the
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\series bold
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Cairo
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\series default
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package.
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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status open
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<<cairo-png-dev, ref.label='test-plot', dev='CairoPNG', out.width='.5
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\backslash
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\backslash
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linewidth', echo=FALSE>>=
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@
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\end_inset
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\end_layout
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\begin_layout Section
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Plot Recording
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\end_layout
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\begin_layout Standard
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As mentioned in the main manual,
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\series bold
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knitr
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\series default
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uses the
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\series bold
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evaluate
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\series default
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package to record plots.
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There are two sources of plots: first, whenever
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\emph on
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plot.new()
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\emph default
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or
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\emph on
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grid.newpage()
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\emph default
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is called,
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\series bold
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evaluate
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\series default
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will try to save a snapshot of the current plot
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\begin_inset Foot
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status open
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\begin_layout Plain Layout
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For technical details, see
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?setHook
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\family default
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and
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\family typewriter
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?recordPlot
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\end_layout
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\end_inset
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; second, after each complete expression is evaluated, a snapshot is also
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saved.
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To speed up recording, the null graphical device
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\family typewriter
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pdf(file = NULL)
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\family default
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is used.
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Figure
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\begin_inset CommandInset ref
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LatexCommand ref
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reference "fig:two-high"
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\end_inset
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shows two expressions producing two high-level plots.
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\end_layout
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wide false
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status open
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<<two-high, fig.width=3, fig.height=2.5, out.width='.49
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\backslash
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\backslash
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linewidth'>>=
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\end_layout
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\begin_layout Plain Layout
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plot(cars)
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\end_layout
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boxplot(cars$dist,xlab='dist')
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\end_layout
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\begin_layout Plain Layout
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@
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Two high-level plots are captured.
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The key to arrange two plots side by side is to specify the
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\family typewriter
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out.width
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\family default
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option so that each plot takes less than half of the line width.
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We do not have to use the
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\family typewriter
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par(mfrow)
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\family default
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trick, and it may not work in some cases (e.g.
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to put base graphics and
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\series bold
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ggplot2
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\series default
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side by side; recall Figure 1 in the main manual).
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\begin_inset CommandInset label
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LatexCommand label
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name "fig:two-high"
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\end_inset
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\end_layout
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\begin_layout Standard
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Figure
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\begin_inset CommandInset ref
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LatexCommand ref
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reference "fig:low-plot-loop"
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\end_inset
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shows another example of two R expressions, but the second expression only
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involves with low-level plotting changes.
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By default, low-level plot changes are discarded, but you can retain them
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with the option
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\family typewriter
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fig.keep='all'
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\family default
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.
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\end_layout
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\begin_layout Standard
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wide false
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<<low-plot-loop, fig.width=3, fig.height=2.5, out.width='.49
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\backslash
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\backslash
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linewidth', fig.keep='all'>>=
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\end_layout
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\begin_layout Plain Layout
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plot(0,0,type='n',ann=FALSE)
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\end_layout
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\begin_layout Plain Layout
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for(i in seq(0, 2*pi,length=20)) {points(cos(i),sin(i))}
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\end_layout
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\begin_layout Plain Layout
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@
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\begin_layout Plain Layout
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\begin_inset Caption Standard
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\begin_layout Plain Layout
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Two complete R expressions will produce at most two plots, as long as there
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are not multiple high-level plotting calls in each expression; option
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\family typewriter
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fig.keep='all'
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\family default
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here.
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\begin_inset CommandInset label
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LatexCommand label
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name "fig:low-plot-loop"
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\end_inset
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\begin_layout Standard
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Together with
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\family typewriter
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fig.show='asis'
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\family default
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, we can show the process of plotting step by step like Figure
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\begin_inset CommandInset ref
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LatexCommand ref
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reference "fig:high-with-low"
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\end_inset
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.
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\end_layout
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\begin_layout Standard
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\begin_inset Float figure
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wide false
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sideways false
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status open
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\begin_layout Plain Layout
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\begin_inset ERT
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status open
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<<high-with-low, fig.width=3, fig.height=2.5, out.width='.5
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\backslash
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\backslash
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linewidth', fig.keep='all', fig.show='asis'>>=
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\end_layout
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|
\begin_layout Plain Layout
|
|
|
|
plot(cars)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
abline(lm(dist~speed, data=cars)) # a regression line
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
Low-level plot changes in base graphics can be recorded separately, and
|
|
plots can be put in the places where they were produced.
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "fig:high-with-low"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
A further note on plot recording:
|
|
\series bold
|
|
knitr
|
|
\series default
|
|
examines all recorded plots (as R objects) and compares them sequentially;
|
|
if the previous plot is a
|
|
\begin_inset Quotes eld
|
|
\end_inset
|
|
|
|
subset
|
|
\begin_inset Quotes erd
|
|
\end_inset
|
|
|
|
of the next plot (= previous plot + low-level changes), the previous plot
|
|
will be removed when
|
|
\family typewriter
|
|
fig.keep='high'
|
|
\family default
|
|
.
|
|
If two successive plots are identical, the second one will be removed by
|
|
default, so it might be a little bit surprising that the following chunk
|
|
will only produce one plot by default
|
|
\begin_inset Foot
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
adapted from
|
|
\begin_inset Flex URL
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
https://github.com/yihui/knitr/issues/41
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
:
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<identical-plots,eval=FALSE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
m = matrix(1:100, ncol = 10)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
image(m)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
image(m*2) # exactly the same as previous plot
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
Plot Rearrangement
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
We can rearrange the plots in chunks in several ways.
|
|
They can be inserted right after the line(s) of R code which produced them,
|
|
or accumulated till the end of the chunk.
|
|
There is an example in the main manual demonstrating
|
|
\family typewriter
|
|
fig.show='asis'
|
|
\family default
|
|
for two high-level plots, and Figure
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:high-with-low"
|
|
|
|
\end_inset
|
|
|
|
in this manual also demonstrates this option for a high-level plot followed
|
|
by a low-level change.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Here is an example demonstrating the option
|
|
\family typewriter
|
|
fig.keep='last'
|
|
\family default
|
|
(only the last plot is kept):
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float figure
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<fig-last, fig.width=5.2, fig.height=3, out.width='.7
|
|
\backslash
|
|
|
|
\backslash
|
|
linewidth', fig.keep='last', message=FALSE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
library(ggplot2)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
pie <- ggplot(diamonds, aes(x = factor(1), fill = cut)) + xlab('cut') +
|
|
geom_bar(width = 1)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
pie + coord_polar(theta = "y") # a pie chart
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
pie + coord_polar() # the bullseye chart
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
Two plots were produced in this chunk, but only the last one is kept.
|
|
This can be useful when we experiment with many plots, but only want the
|
|
last result.
|
|
(Adapted from the
|
|
\series bold
|
|
ggplot2
|
|
\series default
|
|
website)
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
When multiple plots are produced by a code chunk, we may want to show them
|
|
as an animation with the option
|
|
\family typewriter
|
|
fig.show='animate'
|
|
\family default
|
|
.
|
|
Figure
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:clock-animation"
|
|
|
|
\end_inset
|
|
|
|
shows a simple clock animation; you may compare the code to Figure
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:high-with-low"
|
|
|
|
\end_inset
|
|
|
|
to understand that high-level plots are always recorded, regardless of
|
|
where they appeared.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float figure
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<clock-animation, fig.width=3, fig.height=3, out.width='.4
|
|
\backslash
|
|
|
|
\backslash
|
|
linewidth', fig.show='animate', tidy=FALSE, crop=TRUE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
par(mar = rep(3, 4))
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
for (i in seq(pi/2, -4/3 * pi, length = 12)) {
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
plot(0, 0, pch = 20, ann = FALSE, axes = FALSE)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
arrows(0, 0, cos(i), sin(i))
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
axis(1, 0, "VI"); axis(2, 0, "IX")
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
axis(3, 0, "XII"); axis(4, 0, "III"); box()
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
A clock animation.
|
|
You have to view it in Adobe Reader: click to play/pause; there are also
|
|
buttons to speed up or slow down the animation.
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "fig:clock-animation"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
We can also set the alignment of plots easily with the
|
|
\family typewriter
|
|
fig.align
|
|
\family default
|
|
option; this document uses
|
|
\family typewriter
|
|
fig.align='center'
|
|
\family default
|
|
as a global option, and we can also set plots to be left/right-aligned.
|
|
Figure
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:maruko-plot"
|
|
|
|
\end_inset
|
|
|
|
is an example of a left-aligned plot.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float figure
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<maruko-plot, fig.width=7, fig.height=4, out.width='.45
|
|
\backslash
|
|
|
|
\backslash
|
|
linewidth', fig.align='left', crop=TRUE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
stars(cbind(1:16,10*(16:1)),draw.segments=TRUE)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
A left-aligned plot adapted from
|
|
\family typewriter
|
|
?stars
|
|
\family default
|
|
(I call this the
|
|
\begin_inset Quotes eld
|
|
\end_inset
|
|
|
|
Maruko
|
|
\begin_inset Quotes erd
|
|
\end_inset
|
|
|
|
plot, and it is one of my favorites; see
|
|
\begin_inset Flex URL
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
http://en.wikipedia.org/wiki/Chibi_Maruko-chan
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
).
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "fig:maruko-plot"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
Plot Size
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
We have seen several examples in which two or more plots can be put side
|
|
by side, and this is because the plots were resized in the output document;
|
|
with the chunk option
|
|
\family typewriter
|
|
out.width
|
|
\family default
|
|
less than half of the line width, LaTeX will arrange two plots in one line;
|
|
if it is less than
|
|
\begin_inset Formula $1/3$
|
|
\end_inset
|
|
|
|
of the line width, three plots can be put in one line.
|
|
Of course we can also set it to be an absolute width like
|
|
\family typewriter
|
|
3in
|
|
\family default
|
|
(3 inches).
|
|
This option is used extensively in this document to control the size of
|
|
plots in the output document.
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
The tikz Device
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
The main advantage of using tikz graphics is the consistency of styles between
|
|
texts in plots and those in the main document.
|
|
Since we can use native LaTeX commands in plots, the styles of texts in
|
|
plots can be very sophisticated (see Figure
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:math-formula-tt"
|
|
|
|
\end_inset
|
|
|
|
for an example).
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float figure
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<math-formula-tt, fig.width=6, fig.height=2, out.width='
|
|
\backslash
|
|
|
|
\backslash
|
|
linewidth'>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
plot(0:1,0:1,type='n', ylab='origin of statistics', xlab='statistical presentati
|
|
on rocks with
|
|
\backslash
|
|
|
|
\backslash
|
|
LaTeX{}')
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
text(.5,c(.8,.5,.2), c('
|
|
\backslash
|
|
|
|
\backslash
|
|
texttt{lm(y
|
|
\backslash
|
|
|
|
\backslash
|
|
textasciitilde{} x)}', '$
|
|
\backslash
|
|
|
|
\backslash
|
|
hat{
|
|
\backslash
|
|
|
|
\backslash
|
|
beta}=(X^{
|
|
\backslash
|
|
|
|
\backslash
|
|
prime}X)^{-1}X^{
|
|
\backslash
|
|
|
|
\backslash
|
|
prime}y$', '$(
|
|
\backslash
|
|
|
|
\backslash
|
|
Omega,
|
|
\backslash
|
|
|
|
\backslash
|
|
mathcal{F},
|
|
\backslash
|
|
|
|
\backslash
|
|
mu)$'))
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
A plot created by
|
|
\series bold
|
|
tikzDevice
|
|
\series default
|
|
with math expressions and typewriter fonts.
|
|
Note the font style consistency -- we write the same expressions in LaTeX
|
|
here:
|
|
\begin_inset Formula $\hat{\beta}=(X^{\prime}X)^{-1}X^{\prime}y$
|
|
\end_inset
|
|
|
|
and
|
|
\begin_inset Formula $(\Omega,\mathcal{F},\mu)$
|
|
\end_inset
|
|
|
|
; also
|
|
\family typewriter
|
|
lm(y ~ x)
|
|
\family default
|
|
.
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "fig:math-formula-tt"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
When using XeLaTeX instead of PDFLaTeX to compile the document, we need
|
|
to tell the
|
|
\series bold
|
|
tikzDevice
|
|
\series default
|
|
package by setting the
|
|
\family typewriter
|
|
tikzDefaultEngine
|
|
\family default
|
|
option before all plot chunks (preferably in the first chunk):
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<xetex-tikz, eval=FALSE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
options(tikzDefaultEngine='xetex')
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
This is useful and often necessary to compile tikz plots which contain (UTF8)
|
|
multi-byte characters.
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
Figure Caption
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
If the chunk option
|
|
\family typewriter
|
|
fig.cap
|
|
\family default
|
|
is not
|
|
\family typewriter
|
|
NULL
|
|
\family default
|
|
or
|
|
\family typewriter
|
|
NA
|
|
\family default
|
|
, the plots will be put in a
|
|
\family typewriter
|
|
figure
|
|
\family default
|
|
environment when the output format is LaTeX, and this option is used to
|
|
write a caption in this environment using
|
|
\family typewriter
|
|
|
|
\backslash
|
|
caption{}
|
|
\family default
|
|
.
|
|
The other two related options are
|
|
\family typewriter
|
|
fig.scap
|
|
\family default
|
|
and
|
|
\family typewriter
|
|
fig.lp
|
|
\family default
|
|
which set the short caption and a prefix string for the figure label.
|
|
The default short caption is extracted from the caption by truncating it
|
|
at the first period or colon or semi-colon.
|
|
The label is a combination of
|
|
\family typewriter
|
|
fig.lp
|
|
\family default
|
|
and the chunk label.
|
|
Because
|
|
\family typewriter
|
|
figure
|
|
\family default
|
|
is a float environment, it can float away from the chunk output to other
|
|
places such as the top or bottom of a page when the TeX document is compiled.
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
Other Features
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
The
|
|
\series bold
|
|
knitr
|
|
\series default
|
|
package can be extended with hook functions, and here I give a few examples
|
|
illustrating the flexibility.
|
|
\end_layout
|
|
|
|
\begin_layout Subsection
|
|
Cropping PDF Graphics
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Some R users may have been suffering from the extra margins in R plots,
|
|
especially in base graphics (
|
|
\series bold
|
|
ggplot2
|
|
\series default
|
|
is much better in this aspect).
|
|
The default graphical option
|
|
\family typewriter
|
|
mar
|
|
\family default
|
|
is about
|
|
\family typewriter
|
|
c(5, 4, 4, 2)
|
|
\family default
|
|
(see
|
|
\family typewriter
|
|
?par
|
|
\family default
|
|
), which is often too big.
|
|
Instead of endlessly setting
|
|
\family typewriter
|
|
par(mar)
|
|
\family default
|
|
, you may consider the program
|
|
\family typewriter
|
|
pdfcrop
|
|
\family default
|
|
, which can crop the white margin automatically
|
|
\begin_inset Foot
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Flex URL
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
http://www.ctan.org/pkg/pdfcrop
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
.
|
|
In
|
|
\series bold
|
|
knitr
|
|
\series default
|
|
, we can set up the hook
|
|
\emph on
|
|
hook_pdfcrop()
|
|
\emph default
|
|
to work with a chunk option, say,
|
|
\family typewriter
|
|
crop
|
|
\family default
|
|
.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<crop-hook, cache=FALSE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
knit_hooks$set(crop=hook_pdfcrop)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Now we compare two plots below.
|
|
The first one is not cropped (Figure
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:pdf-nocrop"
|
|
|
|
\end_inset
|
|
|
|
); then the same plot is produced but with a chunk option
|
|
\family typewriter
|
|
crop=TRUE
|
|
\family default
|
|
which will call the cropping hook (Figure
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:pdf-crop"
|
|
|
|
\end_inset
|
|
|
|
).
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float figure
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
begin{kframe}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<pdf-nocrop, fig.width=3.2, fig.height=3.2, out.width='.5
|
|
\backslash
|
|
|
|
\backslash
|
|
linewidth'>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
par(mar=c(5,4,4,2),bg='white') # large margin
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
plot(lat~long,data=quakes,pch=20,col=rgb(0,0,0,.2))
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
end{kframe}
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
The original plot produced in R, with a large margin.
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "fig:pdf-nocrop"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float figure
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
begin{kframe}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<pdf-crop, ref.label='pdf-nocrop', echo=FALSE, fig.width=3.2, fig.height=3.2,
|
|
out.width='.5
|
|
\backslash
|
|
|
|
\backslash
|
|
linewidth', crop=TRUE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
end{kframe}
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
The cropped plot; it fits better in the document.
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "fig:pdf-crop"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
As we can see, the white margins are gone.
|
|
If we use
|
|
\emph on
|
|
par()
|
|
\emph default
|
|
, it might be hard and tedious to figure out a reasonable amount of margin
|
|
in order that neither is any label cropped nor do we get a too large margin.
|
|
My experience is that
|
|
\family typewriter
|
|
pdfcrop
|
|
\family default
|
|
works well with base graphics, but barely works with
|
|
\series bold
|
|
grid
|
|
\series default
|
|
graphics (therefore
|
|
\series bold
|
|
lattice
|
|
\series default
|
|
and
|
|
\series bold
|
|
ggplot2
|
|
\series default
|
|
are ruled out).
|
|
\end_layout
|
|
|
|
\begin_layout Subsection
|
|
Manually Saved Plots
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
We have explained how R plots are recorded before.
|
|
In some cases, it is not possible to capture plots by
|
|
\emph on
|
|
recordPlot()
|
|
\emph default
|
|
(such as
|
|
\series bold
|
|
rgl
|
|
\series default
|
|
plots), but we can save them using other functions.
|
|
To insert these plots into the output, we need to set up a hook first like
|
|
this (see
|
|
\family typewriter
|
|
?hook_plot_custom
|
|
\family default
|
|
for details):
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<custom-plot-hook, cache=FALSE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
knit_hooks$set(custom.plot = hook_plot_custom)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Then we set the chunk option
|
|
\family typewriter
|
|
custom.plot=TRUE
|
|
\family default
|
|
, and manually write plot files in the chunk.
|
|
Here we show an example of capturing GGobi plots using the function
|
|
\emph on
|
|
ggobi_display_save_picture()
|
|
\emph default
|
|
in the
|
|
\series bold
|
|
rggobi
|
|
\series default
|
|
package:
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<ggobi-plot, custom.plot=TRUE, fig.ext='png', out.width='2.5in', results='hide',
|
|
warning=FALSE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
library(rggobi)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
ggobi(ggobi_find_file('data', 'flea.csv'))
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
Sys.sleep(1) # wait for snapshot
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
ggobi_display_save_picture(path=fig_path('.png'))
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
One thing to note here is we have to make sure the plot filename is from
|
|
|
|
\emph on
|
|
fig_path()
|
|
\emph default
|
|
, which is a convenience function to return the figure path for the current
|
|
chunk.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
We can do whatever normal R plots can do with this hook, and we give another
|
|
example below to show how to work with animations.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<rgl-animation, custom.plot=TRUE, fig.ext='png', out.width='2.5in', fig.show='animat
|
|
e', fig.num=20, interval=.4, aniopts='controls,autoplay', results='hide',
|
|
warning=FALSE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
library(animation) # adapted from demo('rgl_animation')
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
data(pollen)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
uM = matrix(c(-0.37, -0.51, -0.77, 0, -0.73, 0.67, -0.1, 0, 0.57, 0.53, -0.63, 0,
|
|
0, 0, 0, 1), 4, 4)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
library(rgl)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
open3d(userMatrix = uM, windowRect = c(0, 0, 400, 400))
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
plot3d(pollen[, 1:3])
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
zm = seq(1, 0.05, length = 20)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
par3d(zoom = 1) # change the zoom factor gradually later
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
for (i in 1:length(zm)) {
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
par3d(zoom = zm[i]); Sys.sleep(.05)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
rgl.snapshot(fig_path('png', number = i))
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Subsection
|
|
rgl Plots
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
With the hook
|
|
\emph on
|
|
hook_rgl()
|
|
\emph default
|
|
, we can easily save snapshots from the
|
|
\series bold
|
|
rgl
|
|
\series default
|
|
package.
|
|
We have shown an example in the main manual, and here we add some details.
|
|
The rgl hook is a good example of taking care of details by carefully using
|
|
the
|
|
\family typewriter
|
|
options
|
|
\family default
|
|
argument in the hook; for example, we cannot directly set the width and
|
|
height of rgl plots in
|
|
\emph on
|
|
rgl.snapshot()
|
|
\emph default
|
|
or
|
|
\emph on
|
|
rgl.postscript()
|
|
\emph default
|
|
, so we make use of the options
|
|
\family typewriter
|
|
fig.width
|
|
\family default
|
|
,
|
|
\family typewriter
|
|
fig.height
|
|
\family default
|
|
and
|
|
\family typewriter
|
|
dpi
|
|
\family default
|
|
to calculate the expected size of the window, then resize the current window
|
|
by
|
|
\emph on
|
|
par3d()
|
|
\emph default
|
|
, and finally save the plot.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
This hook is actually built upon
|
|
\emph on
|
|
hook_plot_custom()
|
|
\emph default
|
|
-- first it saves the
|
|
\series bold
|
|
rgl
|
|
\series default
|
|
snapshot, then it calls
|
|
\emph on
|
|
hook_plot_custom()
|
|
\emph default
|
|
to write the output code.
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
\start_of_appendix
|
|
How to Compile This Manual
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
This manual has a long chain of dependencies, so it may not be easy to compile.
|
|
These packages are required (all of them are free software):
|
|
\end_layout
|
|
|
|
\begin_layout Description
|
|
R Cairo, ggplot2, tikzDevice, rgl, rggobi, animation (all available on CRAN
|
|
except tikzDevice which is on R-Forge for the time being)
|
|
\end_layout
|
|
|
|
\begin_layout Description
|
|
LaTeX animate, hyperref and the tufte-handout class
|
|
\end_layout
|
|
|
|
\begin_layout Description
|
|
Other GGobi, pdfcrop
|
|
\end_layout
|
|
|
|
\end_body
|
|
\end_document
|