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knitr-graphics.lyx
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#LyX 2.1 created this file. For more info see http://www.lyx.org/
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\begin_document
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\begin_body
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<setup, include=FALSE, cache=FALSE>>=
\end_layout
\begin_layout Plain Layout
library(knitr)
\end_layout
\begin_layout Plain Layout
options(formatR.arrow=TRUE,width=50)
\end_layout
\begin_layout Plain Layout
opts_chunk$set(fig.path='figure/graphics-', cache.path='cache/graphics-',
fig.align='center', dev='tikz', fig.width=5, fig.height=5, fig.show='hold',
cache=TRUE, par=TRUE)
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knit_hooks$set(par=function(before, options, envir){
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@
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\begin_layout Title
knitr Graphics Manual
\end_layout
\begin_layout Author
Yihui Xie
\end_layout
\begin_layout Abstract
This manual shows features of graphics in the
\series bold
knitr
\series default
package (version
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
Sexpr{packageVersion('knitr')}
\end_layout
\end_inset
) in detail, including the graphical devices, plot recording, plot rearrangement
, control of plot sizes, the tikz device, figure captions, animations and
other types of plots such as
\series bold
rgl
\series default
or GGobi plots.
\end_layout
\begin_layout Standard
Before reading this specific manual
\begin_inset Foot
status open
\begin_layout Plain Layout
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://bit.ly/knitr-graphics-src
\end_layout
\end_inset
(Rnw source)
\end_layout
\end_inset
, you must have finished the main manual
\begin_inset Foot
status open
\begin_layout Plain Layout
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://bit.ly/knitr-main
\end_layout
\end_inset
\end_layout
\end_inset
.
\end_layout
\begin_layout Section
Graphical Devices
\end_layout
\begin_layout Standard
The
\series bold
knitr
\series default
package comes with more than 20 built-in graphical devices, and you can
specify them through the
\family typewriter
dev
\family default
option.
This document uses the global option
\family typewriter
dev='tikz'
\family default
, i.e., the plots are recorded by the tikz device by default, but we can change
the device locally.
Since tikz will be used extensively throughout this manual and you will
see plenty of tikz graphics later, now we first show a few other devices.
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<test-plot, eval=FALSE>>=
\end_layout
\begin_layout Plain Layout
with(trees, symbols(Height, Volume, circles = Girth/16, inches = FALSE,
bg = 'deeppink', fg = 'gray30'))
\end_layout
\begin_layout Plain Layout
@
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\end_inset
\end_layout
\begin_layout Standard
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<<pdf-dev, ref.label='test-plot', dev='pdf', out.width='
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@
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\begin_layout Plain Layout
\begin_inset Caption Standard
\begin_layout Plain Layout
The default PDF device.
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LatexCommand label
name "mar:pdf-dev"
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\begin_layout Standard
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<<png-dev, ref.label='test-plot', dev='png', out.width='
\backslash
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linewidth', echo=FALSE>>=
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@
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\end_inset
\end_layout
\begin_layout Plain Layout
\begin_inset Caption Standard
\begin_layout Plain Layout
The PNG device.
\begin_inset CommandInset label
LatexCommand label
name "mar:png-dev"
\end_inset
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "mar:pdf-dev"
\end_inset
and
\begin_inset CommandInset ref
LatexCommand ref
reference "mar:png-dev"
\end_inset
show two standard devices in the
\series bold
grDevices
\series default
package.
We can also use devices in the
\series bold
Cairo
\series default
or
\series bold
cairoDevice
\series default
package, e.g., the chunk below uses the
\emph on
CairoPNG()
\emph default
device in the
\series bold
Cairo
\series default
package.
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<cairo-png-dev, ref.label='test-plot', dev='CairoPNG', out.width='.5
\backslash
\backslash
linewidth', echo=FALSE>>=
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Section
Plot Recording
\end_layout
\begin_layout Standard
As mentioned in the main manual,
\series bold
knitr
\series default
uses the
\series bold
evaluate
\series default
package to record plots.
There are two sources of plots: first, whenever
\emph on
plot.new()
\emph default
or
\emph on
grid.newpage()
\emph default
is called,
\series bold
evaluate
\series default
will try to save a snapshot of the current plot
\begin_inset Foot
status open
\begin_layout Plain Layout
For technical details, see
\family typewriter
?setHook
\family default
and
\family typewriter
?recordPlot
\end_layout
\end_inset
; second, after each complete expression is evaluated, a snapshot is also
saved.
To speed up recording, the null graphical device
\family typewriter
pdf(file = NULL)
\family default
is used.
Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:two-high"
\end_inset
shows two expressions producing two high-level plots.
\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
<<two-high, fig.width=3, fig.height=2.5, out.width='.49
\backslash
\backslash
linewidth'>>=
\end_layout
\begin_layout Plain Layout
plot(cars)
\end_layout
\begin_layout Plain Layout
boxplot(cars$dist,xlab='dist')
\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 high-level plots are captured.
The key to arrange two plots side by side is to specify the
\family typewriter
out.width
\family default
option so that each plot takes less than half of the line width.
We do not have to use the
\family typewriter
par(mfrow)
\family default
trick, and it may not work in some cases (e.g.
to put base graphics and
\series bold
ggplot2
\series default
side by side; recall Figure 1 in the main manual).
\begin_inset CommandInset label
LatexCommand label
name "fig:two-high"
\end_inset
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:low-plot-loop"
\end_inset
shows another example of two R expressions, but the second expression only
involves with low-level plotting changes.
By default, low-level plot changes are discarded, but you can retain them
with the option
\family typewriter
fig.keep='all'
\family default
.
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
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\begin_inset ERT
status open
\begin_layout Plain Layout
<<low-plot-loop, fig.width=3, fig.height=2.5, out.width='.49
\backslash
\backslash
linewidth', fig.keep='all'>>=
\end_layout
\begin_layout Plain Layout
plot(0,0,type='n',ann=FALSE)
\end_layout
\begin_layout Plain Layout
for(i in seq(0, 2*pi,length=20)) {points(cos(i),sin(i))}
\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 complete R expressions will produce at most two plots, as long as there
are not multiple high-level plotting calls in each expression; option
\family typewriter
fig.keep='all'
\family default
here.
\begin_inset CommandInset label
LatexCommand label
name "fig:low-plot-loop"
\end_inset
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Together with
\family typewriter
fig.show='asis'
\family default
, we can show the process of plotting step by step like Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:high-with-low"
\end_inset
.
\end_layout
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wide false
sideways false
status open
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status open
\begin_layout Plain Layout
<<high-with-low, fig.width=3, fig.height=2.5, out.width='.5
\backslash
\backslash
linewidth', fig.keep='all', fig.show='asis'>>=
\end_layout
\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