[R] Knitr, ggplot and consistent fonts
Duncan Murdoch
murdoch.duncan at gmail.com
Mon Dec 23 21:52:32 CET 2013
On 13-12-23 1:07 PM, John Kane wrote:
> Thanks Duncan.
> I had the feeling I was doing something wrong but did not realise it was that stupid.
>
> showNonASCII('ggplot(df, aes(x = x)) + geom_histogram(aes(y = ..density..)),
> binwidth = 1, colour = "black", fill = "white")')
>
> now runs and does what the help page seems to imply: Nothing.
>
> From the showNonASCII help page:
> "The elements of x containing non-ASCII characters will be returned invisibly."
>
> One gets a result one does not see? Does one have to explicitly capture the result somehow? I really have not the faintest idea of what the example from the help page is doing.
"returned invisibly" means that the result is returned with a flag set
so it won't automatically print. If you want to print it, you need to
ask. So any of these will work to see the result:
x <- showNonASCII( .... )
x
or
print(showNonASCII( .... ))
or even (though this is one some of us don't like, it still works...)
(showNonASCII( .... ))
Duncan Murdoch
> John Kane
> Kingston ON Canada
>
>
>> -----Original Message-----
>> From: murdoch.duncan at gmail.com
>> Sent: Mon, 23 Dec 2013 12:51:43 -0500
>> To: jrkrideau at inbox.com, rmh at temple.edu
>> Subject: Re: [R] Knitr, ggplot and consistent fonts
>>
>> On 13-12-23 12:40 PM, John Kane wrote:
>>> Thanks Richard. I did not realise such a function existed.
>>>
>>> Assuming I am using it correctly I do get an error though not where I
>>> was expecting it. Anyway the code below returns an error
>>>
>>> library(tools)
>>> showNonASCII("ggplot(df, aes(x = x)) + geom_histogram(aes(y =
>>> ..density..)), binwidth = 1, colour = "black", fill = "white")")
>>>
>>> Results
>>> Error: unexpected symbol in:
>>> "showNonASCII("ggplot(df, aes(x = x)) + geom_histogram(aes(y =
>>> ..density..)), binwidth = 1, colour = "black"
>>
>> You get that error because you're using double quotes around a string
>> containing double quotes, and not escaping them. With that string,
>> using single quotes on the outside should be fine:
>>
>> showNonASCII('ggplot(df, aes(x = x)) + geom_histogram(aes(y =
>> ..density..)), binwidth = 1, colour = "black", fill = "white")')
>>
>> Duncan Murdoch
>>>
>>>
>>>
>>> John Kane
>>> Kingston ON Canada
>>>
>>>
>>>> -----Original Message-----
>>>> From: rmh at temple.edu
>>>> Sent: Mon, 23 Dec 2013 11:44:42 -0500
>>>> To: jrkrideau at inbox.com
>>>> Subject: Re: [R] Knitr, ggplot and consistent fonts
>>>>
>>>> If the problem seems to be non-ASCII characters, then the first
>>>> investigation
>>>> step is to use the R functions
>>>>
>>>> ?tools::showNonASCII
>>>> ?tools::showNonASCIIfile
>>>>
>>>> On Mon, Dec 23, 2013 at 11:37 AM, John Kane <jrkrideau at inbox.com>
>>>> wrote:
>>>>> 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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>>>>>> ______________________________________________
>>>>>> 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.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ______________________________________________
>>>>>> 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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>>>>> R-help at r-project.org mailing list
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>>
>
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