[knitr] Graphics: Power of graphics in knitr | /knitr/demo/graphics/

Yes I realized that a few days ago, and I have updated the Rnw source: https://github.com/yihui/knitr/commits/master/inst/examples/knitr-graphics.Rnw

Note the error occurs in Adobe Reader but not in Evince. I do not know why that is the case, but I have found out the reason to be that I used a plot containing Chinese characters, so I removed that chunk, and now if you compile the document again, everything will be fine. Anyway, I will update the PDF document later as well. Thanks a lot!

Originally posted on 2012-04-06 20:54:29

Guest *Rivo* @ 2012-06-11 23:15:22 originally posted:

It works .. rggobi is not available for R2.15.0 so I just commented out that part

Michael Lawrence managed to build the 64bit Windows version of GGobi two weeks ago, and hopefully the Windows version of rggobi will be back on CRAN in the near future.

If you need rggobi only for this manual, you can probably remove that chunk. It was there only for demo purpose.

Originally posted on 2012-06-27 04:05:12

You can see https://gist.github.com/2475551 for an example.

Originally posted on 2012-07-04 23:20:43

Guest *Charles Berry* @ 2012-07-05 14:36:27 originally posted:

Thanks for the quick reply!

 I  ran the code you referenced, but no there were graphics. So I added plot(mpg~disp,df) as the last line of last chunk in template.Rnw. It ran just fine and produced 3 plots.

Then I tried pairs(df) instead of plot(). It produced 6 plots - 3 labelled  run-all[1-3].pdf and 3  gear[3-5]unnamed-chunk-2.pdf and put all of them in the document. Further, the first three looked defective - the lower right panel is missing.

The chunk 'run-all' is not supposed to have graphics output, so you need to put an extra chunk option fig.keep = 'none' to suppress the first three defective plots.

Originally posted on 2012-07-05 17:56:12

In fact I'm curious about the answer too, because I have also been exploring in this direction (e.g. https://github.com/yihui/thesis/blob/master/template.tex). My feeling is that you should not expect too much from the simple markdown format. Raw LaTeX is unbeatable anyway. I guess you have to either give up some fancy LaTeX features to use markdown, or just go back to LaTeX.

For me, whenever I need to write LaTeX, I use LyX. It is as good as Markdown -- easy to read and easy to write; besides, it is essentially LaTeX and the source code is surprisingly clean with unbeatable support to LaTeX math equations. I know many people really do not like it, though. The only disadvantage is you only have PDF output which does not quite fit the web. HTML export from LaTeX often does not look as clean as Markdown.

Originally posted on 2012-07-27 19:33:31

Guest *mrdwab* @ 2012-07-28 04:02:17 originally posted:

I do use LyX, but I really like the integration between document creation and R in RStudio, where I can directly run code from an R markdown code chunk to make sure that everything in that chunk is working as expected. I guess that since I don't use the HTML export too often, it's more of a convenience factor of not having two programs open!

I'll definitely check out your templates though.

At the moment there is no easy way, but it depends on your definition of "easy" -- here is one solution http://stackoverflow.com/q/11915328/559676

Originally posted on 2012-09-21 17:51:28

Guest *Guger* @ 2012-09-22 02:43:09 originally posted:

Thank you for your quick response!
But as far I understand the code, this change in hook behavior
works well only when I have one or two high-level plots per chunk, right?

In my case I have to generate several numbered plots in one chunk in a cycle.... I have tried fig.keep='all', 'high', but neither option resulted in more than two figures inserted.

Would you recommend to use looping approach you described at git://gist.github.com/2475551.git "use knit() with a loop to write reports for subsets of data" or I miss some simpler options here???

In theory all plots should be captured without any special tricks. I need a reproducible example.

Originally posted on 2012-09-22 05:46:38

Guest *Guger* @ 2012-09-22 15:30:15 originally posted:

Here is the code....
It should insert 4 identical plots (fig.keep='all') but inserts 2...
Please, give me advice if it happens due to my immaturity in
using your package which I like a lot!
 
documentclass[a4paper]{article}
usepackage[british]{babel}
usepackage{url}
usepackage{breakurl}
usepackage{graphicx}

begin{document}
title{Data Mining Project Report Template}
author{Guger}
maketitle

<>=
knit_hooks$set(plot = function(x, options) {
  x = paste(x, collapse = '.') # x is file.ext now instead of c(file, ext)
  paste0('end{kframe}', hook_plot_tex(x, options), 'begin{kframe}')
})
@

<<plot-loop, dev="pdf" ,="" fig.width="3," fig.height="2.5,out.width='linewidth'," fig.keep="all">>=
for(i in 1:4)
{boxplot(cars$dist,xlab='dist')}
@

end{document}

Guest *Guger* @ 2012-09-22 17:36:06 originally posted:

In my code it is a correct line, I paste it here - still correct line, when I push "Post as" - it becomes rearranged. Magic! I hope see the cycle and fix the line after copy-paste. Thanks!

Next time you can use pastebin.com or github gists. Disqus is stupid in dealing with program code; you have to escape special HTML characters manually.

For the problem in knitr, it has been explained in the graphics manual: https://github.com/downloads/yihui/knitr/knitr-graphics.pdf Basically all your plots are identical (the for loop does not make much sense), and identical plots are removed by default.

Originally posted on 2012-09-22 17:42:29

Guest *Guger* @ 2012-09-23 17:54:33 originally posted:

 You were right, it works, thanks! I had read the manual, I just thought fig.keep="all" keeps all of them, even identical.

Sorry I did not pay enough attention to fig.keep="all", and your understanding was absolutely correct. It should keep all four plots in theory, but I just realized that this was a feature of the evaluate package, over which I do not have control in knitr.

Anyway, I do not you will really draw identical plots in a loop in practice, so this problem probably will not bite you :)

Originally posted on 2012-09-23 18:39:29

You can redefine the inline hook, e.g. https://github.com/yihui/knitr-examples/blob/master/043-percent.Rnw

In your case you probably want: function(x) paste0('textit{', x, '}')

Originally posted on 2013-01-27 01:55:18

Hi, I have implemented this in the development version: https://github.com/yihui/knitr Thanks!

Originally posted on 2013-02-23 21:41:35

Do not download the web page. Download the GIT repository instead, and find the examples there: https://github.com/yihui/knitr/archive/master.zip

Originally posted on 2013-04-21 01:25:38