[R] Knitr, ggplot and consistent fonts

[John Kane]

Same result here with the same error message mentioned in my first post.  I tried it in Texmaker which is my usual Latex editor, not that I do much in Latex, and then tried it in RStudio and it is still choking.  

Interestingly EMACS will process it and produce a pdf but it simply produces.  It also provides this warning: : Latex Warning; Reference 'fig:plot-figheight' undefined on page 2 on input line 14. 

It seems to repeat the same message for each of the other figures.

John Kane
Kingston ON Canada


> -----Original Message-----
> From: dulcalma at bigpond.com
> Sent: Mon, 23 Dec 2013 22:28:33 +1000
> To: daniel.haugstvedt at gmail.com, r-help at r-project.org
> Subject: Re: [R] Knitr, ggplot and consistent fonts
> 
> Hi Dan
> 
> 
> 
> I think you still have problems with embedded characters or some problems
> in
> char code page conversion or the like.
> 
> 
> 
> Not knowing knitr but Sweave I cobbled the figures manually and ran the
> sweave file to produce the latex file.
> 
> Latex was consistently stopping at the \caption and \ref functions
> 
> I tried to see what was happening I added hyperref & when I copied the
> text
> to hyperref  latex bailed up
> 
> 
> 
> I tried a minimal latex file without problems
> 
> 
> 
> I put the \title etc in the preamble. Some compilers need this
> 
> 
> 
> Duncan
> 
> 
> 
> From: Daniel Haugstvedt [mailto:daniel.haugstvedt at gmail.com]
> Sent: Monday, 23 December 2013 20:10
> To: Duncan Mackay
> Cc: John Kane; R
> Subject: Re: [R] Knitr, ggplot and consistent fonts
> 
> 
> 
> I am really sorry for posting a non-working example. It is running when I
> cut the code from my previous mail into a clean session in RStudio (OSX).
> However, I suspect that you are right. I did cut and paste some code from
> a
> forum yesterday which had characters that had to be replaced. I gave
> emacs a
> try, but could not find the problem there either.
> 
> 
> 
> The code below was pasted though textEdit and converted to plain text. I
> hope this takes care of any embedded characters.
> 
> 
> 
> \documentclass{article}
> 
> \begin{document}
> 
> 
> 
> <<setup, include=FALSE, cache=FALSE>>=
> 
> library(knitr)
> 
> library(ggplot2)
> 
> @
> 
> 
> 
> \title{Knitr and ggplot2}
> 
> \author{Daniel Haugstvedt}
> 
> 
> 
> \maketitle
> 
> 
> 
> There are four plots in this article. Figure \ref{fig:plot-figHeight}
> uses
> 
> the argument fig.height=2.5 while Figures \ref{fig:plot-figWidth}
> 
> used both fig.height=2.5 and fig.width=3. The later option makes the font
> 
> too big.
> 
> 
> 
> An alternative approach is used in Figures  \ref{fig:plot-figOutWidthBig}
> and
> 
>  \ref{fig:plot-figOutWidthSmall}. There the argument out.width is set to
> 
>  12 and 8 cm respectively. This stops the problem of excessively large
> fonts
> 
>  for figures with smaller width, but there is still no consistency
> 
>  across plots in terms o font size.
> 
> 
> 
> <<plot-figHeight, echo=FALSE, fig.height=2.5, fig.cap="Density plot with
> no
> fig.width argument", results='hide', fig.pos='ht'>>=
> 
> df = data.frame(x = rnorm(100), y = 1:100)
> 
> ggplot(df, aes(x = x)) +
> 
>   geom_histogram(aes(y = ..density..),
> 
>                  binwidth = 1, colour = "black", fill = "white") +
> 
>   xlab("Improvement, %") +
> 
>   ylab("Density") +
> 
>   theme_classic()
> 
> @
> 
> 
> 
> <<plot-figWidth, echo=FALSE, fig.height=2.5, fig.width = 3,
> fig.cap="Density
> plot with fig.width=3", fig.pos='ht'>>=
> 
> ggplot(df, aes(x = x)) +
> 
>   geom_histogram(aes(y = ..density..),
> 
>                  binwidth = 1, colour = "black", fill = "white") +
> 
>   xlab("Improvement, %") +
> 
>   ylab("Density") +
> 
>   theme_classic()
> 
> @
> 
> 
> 
> <<plot-figOutWidthBig, echo=FALSE, fig.height=2.5, out.width = "12cm",
> fig.cap="Density plot with out.width=12cm", fig.pos='ht'>>=
> 
> ggplot(df, aes(x = x)) +
> 
>   geom_histogram(aes(y = ..density..),
> 
>                  binwidth = 1, colour = "black", fill = "white") +
> 
>   xlab("Improvement, %") +
> 
>   ylab("Density") +
> 
>   theme_classic()
> 
> @
> 
> 
> 
> <<plot-figOutWidthSmall, echo=FALSE, fig.height=2.5, out.width = "8cm",
> fig.cap="Density plot with out.width=8cm", fig.pos='ht'>>=
> 
> ggplot(df, aes(x = x)) +
> 
>   geom_histogram(aes(y = ..density..),
> 
>                  binwidth = 1, colour = "black", fill = "white") +
> 
>   xlab("Improvement, %") +
> 
>   ylab("Density") +
> 
>   theme_classic()
> 
> @
> 
> 
> 
> \end{document}
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Sun, Dec 22, 2013 at 11:59 PM, Duncan Mackay <dulcalma at bigpond.com>
> wrote:
> 
> Hi Daniel
> I tried it in Sweave after modifying it for Sweave and a similar thing
> for
> Latex but R crashed.
> 
> I think there is an embedded character/s before the first chunk and in
> the
> first chunk.
> 
> Duncan
> 
> Duncan Mackay
> Department of Agronomy and Soil Science
> University of New England
> Armidale NSW 2351
> Email: home: mackay at northnet.com.au
> 
> 
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
> On
> Behalf Of John Kane
> Sent: Monday, 23 December 2013 04:19
> To: Daniel Haugstvedt; r-help at r-project.org
> Subject: Re: [R] Knitr, ggplot and consistent fonts
> 
> Hi Daniel,
> 
> For some reason I cannot get your example to work. The problem is in the
> code chunk but I have no idea what is happening. The code is running
> perfectly in R, itself but LaTeX seems to be choking when it hits the
> first
> ggplot statement, that is the one in <<plot-figHeight>>=
> 
> The message I am getting is: "Missing $ inserted <inserted text> $
> ggplot(df, aes(x=x)) = geom_" and my knowledge of LateX is not enough to
> figure out the problem.
> 
> I tried stripping out most of the LaTeX specific verbiage in the code
> chunk
> and running the code in LyX which I use rather than plain vanilla LaTeX
> and
> I still cannot get it to work. It is almost as if there is some hidden
> character in the in that piece of code since I can duplicate the code
> myself
> and I even pasted in most of the geom_histogram code into my code chunk
> and
> it runs.
> 
> John Kane
> Kingston ON Canada
> 
> 
>> -----Original Message-----
>> From: daniel.haugstvedt at gmail.com
>> Sent: Sun, 22 Dec 2013 12:42:50 +0100
>> To: r-help at r-project.org
>> Subject: [R] Knitr, ggplot and consistent fonts
>> 
>> Dear R-help
>> 
>> I am using Knitr and ggplot to draft an article and have now started
>> to improve on the layout and graphics. So far I have not been able to
>> maintain the same font size for labels in all my figures.
>> 
>> My goal is to be able to change the width of the figures while
>> maintaining the same font. This works for the height parameter
>> (example not included).
>> 
>> In the true document I also use tikz, but the problem can be
>> reproduced without it.
>> 
>> I know the question is very specific, but my understanding is that
>> this combination of packages  is common. (They are really great. Keep
>> up the good work.)  There has to be others facing the same problem and
>> someone must have found a nice solution.
>> 
>> Additional attempts from my side which failed are not included in the
>> example. I have tested the Google results i could find without any luck.
>> 
>> Cheers
>> Daniel
>> 
>> PS. I know the example plots could have been smaller, but they just
>> became too ugly for me
>> 
>> 
>> \documentclass{article}
>> \begin{document}
>> 
>> <<setup, include=FALSE, cache=FALSE>>=
>> library(knitr)
>> library(ggplot2)
>> @
>> 
>> \title{Knitr and ggplot2}
>> \author{Daniel Haugstvedt}
>> 
>> \maketitle
>> 
>> There are four plots in this article. Figure \ref{fig:plot-figHeight}
>> uses the argument fig.height=2.5 while Figures \ref{fig:plot-figWidth}
>> used both fig.height=2.5 and fig.width=3. The later option makes the
>> font too big.
>> 
>> An alternative approach is used in Figures
>> \ref{fig:plot-figOutWidthBig} and  \ref{fig:plot-figOutWidthSmall}.
>> There the argument out.width is set to
>>  12 and 8 cm respectively. This stops the problem of excessively large
>> fonts  for figures with smaller width, but there is still no
>> consistency  across plots in terms of font size.
>> 
>> <<plot-figHeight, echo=FALSE, fig.height=2.5, fig.cap="Density plot
>> with no fig.width argument", fig.pos='ht'>>= df = data.frame(x =
>> rnorm(100), y = 1:100) ggplot(df, aes(x = x)) +
>>   geom_histogram(aes(y = ..density..),
>>                  binwidth = 1, colour = "black", fill = "white") +
>>   xlab("Improvement, %") +
>>   ylab("Density") +
>>   theme_classic()
>> @
>> 
>> <<plot-figWidth, echo=FALSE, fig.height=2.5, fig.width = 3,
>> fig.cap="Density plot with fig.width=3", fig.pos='ht'>>= ggplot(df,
>> aes(x = x)) +
>>   geom_histogram(aes(y = ..density..),
>>                  binwidth = 1, colour = "black", fill = "white") +
>>   xlab("Improvement, %") +
>>   ylab("Density") +
>>   theme_classic()
>> @
>> 
>> <<plot-figOutWidthBig, echo=FALSE, fig.height=2.5, out.width = "12cm",
>> fig.cap="Density plot with out.width=12cm", fig.pos='ht'>>= ggplot(df,
>> aes(x = x)) +
>>   geom_histogram(aes(y = ..density..),
>>                  binwidth = 1, colour = "black", fill = "white") +
>>   xlab("Improvement, %") +
>>   ylab("Density") +
>>   theme_classic()
>> @
>> 
>> <<plot-figOutWidthSmall, echo=FALSE, fig.height=2.5, out.width =
>> "8cm", fig.cap="Density plot with out.width=8cm", fig.pos='ht'>>=
>> ggplot(df, aes(x = x)) +
>>   geom_histogram(aes(y = ..density..),
>>                  binwidth = 1, colour = "black", fill = "white") +
>>   xlab("Improvement, %") +
>>   ylab("Density") +
>>   theme_classic()
>> @
>> 
>> \end{document}
>> 
>>       [[alternative HTML version deleted]]
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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