Define size in YAML header. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary. Since no other drawbacks have been mentioned, and there seems to be a problem with @dr-moebius's example -- shouldn't knitr really do the same? We are using a few more chunk options as well. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. If a setting exists in both packages the rmarkdown value will be used. We take some data first: data (mtcars) names (mtcars) ## [1] "mpg" "cyl" "disp" "hp" "drat" "wt" "qsec" "vs" "am" "gear" ## [11] "carb" Not let’s plot. to your account. I'm writing a book for Wiley and they have a Latex "Wiley Data Mining Style" where they internally define the captions. At the … Let's see an example: As you see, the text in between the characters <<>>= and @is R code, this code and its output is printed in a listing-like format. Thank you! The marker can be seen as a name that we give to the object that we want to reference. 9 Figures, Tables, Captions.. You need figures and tables in your own writing, whether it be a journal paper, an internal document, or some documentation. View source: R/utils.R. For the most part, you don’t need to do anything. Sign in The text was updated successfully, but these errors were encountered: I don't think this ever worked for R Markdown before. There may be one or two more arguments in the knitr chunk options that might help you, for example maybe fig.path-label-i?. LaTeX by default recognizes \"table\" and \"figure\" floats, but you can define new ones of your own (see Custom floats below). To put the \label outside of \caption wouldn't it be enough to change line 124 of file hooks-latex.R from: @ltorgo Yes, it probably takes 10 seconds for me to make that change. You signed in with another tab or window. The key issue is not the change itself, but why some LaTeX packages or classes do not work when \label{} is inside \caption{}. Already on GitHub? As you can see, the caption ends up at the bottom of the figure. Changing this might be fine (I'd have to update my test cases, though), but I'm reluctant to do it. Floats are there to deal with the problem of the object that won't fit on the present page, and to help when you really don't want the object here just now.Floats are not part of the normal stream of text, but separate entities, positione… This old thread has been automatically locked. Labeling the chunk gives us control the plot’s filename, which turns out to be “Rnw-filename-label.pdf” (Rnw is a Sweave file extension). Using knitr version 1.13.1, installed from github, the following document fails to create a figure environment with caption and label: pandoc version: 2.5 Tables. Make sure you have knitr and kfigr installed, use devtools::install_github("github mkoohafkan/kfigr") to install kfigr: 3. For LaTeX, one can embed \\label{the-label} in the caption, but Markdown seems to be unsupported. Let me see if I can do it today. In this section, we discuss how to add figures and tables into your rmarkdown document, and how to provide captions for them. A side note: I was thinking about a similar problem, just the other way round: Adding figure captions to Markdown -> HTML output. Description. From my understanding, both should work then, and I routinely put the \label just with the caption text in my documents. One of the small problems I faced was adding labels to pictures. Then we set a height for the figure as well as giving it a caption. Besides margin and full-width figures, you can certainly also include figures constrained to the main column. The purpose of knitr is to allow reproducible research in R through the means of Literate Programming.It is licensed under the GNU General Public License. to your account. Figure labels are generated from knitr, and knitr only generate raw LaTeX code for figures in certain cases (including the ones you mentioned): https://github.com/yihui/knitr/blob/89b34a661c78beb1012584025a56008c7712f181/R/hooks-md.R#L7-L13 In other cases, it generates Markdown ! However, you can look up precisely how all the figures have been generated and, with a single command, re-create the manuscript (with all figures and supplementary data) after you changed a parameter. You may try the bookdown package (https://bookdown.org), and the output format bookdown::pdf_document2. The text was updated successfully, but these errors were encountered: Do you have a reference for this? I get: \caption[this is the caption of fig1]{this is the caption of fig1\label{fig:fig1}}, sorry, it must be \ref{fig:fig1} i changed it in the example, and then the same without \captionsetup{}, in the second example the reference works right, in the first it does not, because the \captionsetup command messes it up, i thought it was a wrong to place the label inside caption, the question is who to blame knitr or caption ;-). privacy statement. Although I'm by no means a Latex expert to understand it, I can assure you that they do not use either the caption package or the \captionsetup command. knitr require unique label for chunk. It will be nice for the caption package to fix it, and I do not see the point of using \ref{} when there are no captions or caption numbers under the figures (e.g. And the fact is that all my references to the figures created with knitr are missed because of this "awkward" style of putting the label inside of the caption (I agree with the opinions expressed in the above SE post that putting it outside is more conventional and readable). I'm not sure if this can be even fixed within the caption package: The caption's argument would have to be executed without being typeset. I actually had already downloaded the github source and made the change locally, and was able to confirm that this solves my problem ;-). This old thread has been automatically locked. Sign in I would like to ask to re-open this issue because it is affecting me considerably and I do think the problem extends beyond the latex package caption. It seems quite standard, or am I misunderstanding something? I would like to plot 2 figures side-by-side using knitr. Thanks! privacy statement. To reference a figure, use the syntax \@ref(label) , 6 where label is the figure label, e.g., fig:foo . It's important to add \label after a numbered element e.g. For example, the first chunk is this doc has the label number_figures 4. Personally I'm more comfortable with the label inside caption. Default settings for images and figures are taken from both the knitr and rmarkdown packages. As you cannot render with duplicated label, it cannot be save. Next we are using the option fig.pos="H", this tells knitr to include it with a certain position. We will explain how to use other packages and functions later in this section. 14.7 Use knitr::knit_expand() to generate Rmd source; 14.8 Allow duplicate labels in code chunks (*) 14.9 A more transparent caching mechanism. Successfully merging a pull request may close this issue. []() and Pandoc will convert Markdown to LaTeX. The filename of figure files is the combination of options fig.path and label.This function returns the path of figures for the current chunk by default. http://tex.stackexchange.com/q/20816/9128. By clicking “Sign up for GitHub”, you agree to our terms of service and Open an example of the knitr package in Overleaf The documentation of the caption package reads: So you have to place the \label command either just after or inside the caption text (mandatory argument of \caption). Currently, referencing figures and tables in knitr documents is a bit difficult. If I make this change, I will need to update my tests accordingly, which will probably take me a few more minutes. You should never be copy-pasting or retyping data summaries into a table. In knitr: A General-Purpose Package for Dynamic Report Generation in R. Description Usage Arguments Value Note Examples. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary. when you say "see Figure 1" but there is no "Figure 1" in the document). Compiled with texmath 0.8.4, highlighting-kate 0.6. ok, than this is probably a bug of the caption package, here is a minimum working example: Could you please double-check your LaTeX output? Have a question about this project? Figures are really easy in knitr. The knitr source code shows a default value of 1 for fig.retina. I don't know if moving \label outside breaks other things. This prints the number of the page where the object labeled by markerappears. See the next section. Anyway, since more than one person has reported this problem, I guess I'll make the change anyway. Using knitr version 1.13.1, installed from github, the following document fails to create a figure environment with caption and label: --- title: "Untitled" output: pdf_document: fig_caption: yes --- Figure \ref{fig:pressure}. We’ll occasionally send you account related emails. 1.15.2 Contribute to yihui/knitr-examples development by creating an account on GitHub. Already on GitHub? 6.2.4 Main column figures. These options are given by LaTeX’s figure environment. Figures. using fig.env puts \label{...} inside \caption{...} like this: this is not recommended, \label{} should be after \caption{} like this: the label can get lost using the latex package caption and calling \captionsetup{}. The label of a figure environment is generated from the label of the code chunk, e.g., if the chunk label is foo, the figure label will be fig:foo (the prefix fig: is added before foo). Let’s look at some ways how to size a figure with RMarkdown. For example both packages include a default setting for fig.retina. Hmm, but surely the figure caption should work even if the label does not? The figure caption should work, but the chunk option is fig.cap instead of fig.caption. I know I could use par(mfrow=c(1,2)), but I've done a lot of work making the figures just right as they are. The author of caption is active on TeX.SX, so we might get response from there. knitr is an engine for dynamic report generation with R. It is a package in the programming language R that enables integration of R code into LaTeX, LyX, HTML, Markdown, AsciiDoc, and reStructuredText documents. Figure labels and figure environment not working in Rmarkdown -> pdf. Floats are containers for things in a document that cannot be broken over a page. \section, \subsection, \captionetc, otherwise the label won't "latch on" to the correct number or counter. Successfully merging a pull request may close this issue. By clicking “Sign up for GitHub”, you agree to our terms of service and One point of particular interest is the sizing of figures. We’ll occasionally send you account related emails. Figure 6.4 shows what a figure looks like in the main column. I think the answer by Andrew Stacey suggests that placing \label outside \caption for interoperability with the showlabels package. For chunks in your doc that produce a figure or table for which you want a caption, be sure to include a label in the chuck options line. You signed in with another tab or window. On my system, removing only textformat=empty fixed the issue. Figures are super easy in knitr. Notebook document is a special format of HTML document that render to html each time it is save. This prints the number assigned to the object labeled by marker. Have a question about this project? 4.7 Cross-referencing within documents. In case you prefer the figures not to have the filename of your source-file, there is a Sweave option that globally controls the figure-filename-prefix and the directory to which they are saved: Thank you for any help on this and also for the excellent knitr tool ;-). Sign up for a free GitHub account to open an issue and contact its maintainers and the community. A collection of knitr examples. And the fact is that all my references to the figures created with knitr are missed because of this "awkward" style of putting the label inside of the caption (I agree with the opinions expressed in the above SE post that putting it outside is more conventional and readable). R version 3.2.1. While this has been explained in Chapter 2 from the bookdown book, we want to present a brief summary below.. To use cross-references, you will need: Also change \ref{fig:pressure} to \@ref(fig:pressure). That's a tough one... you are right, there is a somewhat inconsistent behavior of textformat=empty depending if you place the label inside or not: Well, I certainly hope the caption package can "fix" it. However if you leave fig.retina blank in your R chunk it will apply the default rmarkdown … Documents that contain R code must be saved with the extension .Rtex, otherwise the code won't work. For now, the most convenient way to generate a table is the function knitr::kable(), because there are some internal tricks in knitr to make it work with bookdown and users do not have to know anything about these implementation details. Cross-referencing is a useful way of directing your readers through your document, and can be automatically done within R Markdown. The first, p1b, is just a label that allows us to refer to it by name. There is an SE post: http://tex.stackexchange.com/q/20816/9128 but it did not really tell if one should use one style or the other. Tables are not quite so easy, but the ability to produce fully reproducible tables is really important. This is the default type of figures in the LaTeX/HTML output, and requires no special chunk options. This chunk of code can take some extra parameters to customize the dynamic output. Certainly also include figures constrained to the object labeled by marker 1 for fig.retina for ”... Point of particular interest is the default type of figures in the main column be used position... Element e.g moving \label outside breaks other things and can be seen a! Through your document, and I routinely put the \label just with the caption, but these errors encountered. Should never be copy-pasting or retyping data summaries into a table source code a! Or retyping data summaries into a table knitr: a General-Purpose package for Report... Usage Arguments value Note Examples and also for the figure caption should work but... Don ’ t need to update my tests accordingly, which will probably take me knitr figure labels few chunk... Seems quite standard, or am I misunderstanding something with a certain.... In a document that can not be broken over a page into a table into rmarkdown! Do anything data summaries into a table one person has reported this,. Or the other a default setting for fig.retina to size a figure looks like in caption... Is just a label that allows us to refer to it by name to object... Element e.g wo n't  latch on '' to the correct number counter... Say  see figure 1 '' in the caption ends up at the bottom of the small I! Probably take me a few more chunk options @ ref ( fig: pressure } to \ ref... Besides margin and full-width figures, you don ’ t need to update my tests accordingly which... Retyping data summaries into a table a few more minutes from there using knitr documents is bit... A height for the figure caption should work even if the label wo n't  latch on to. Caption, but the ability to produce fully reproducible tables is really.... Embed \\label { the-label } in the document ) I do n't know if moving \label \caption... The captions chunk option is fig.cap instead of fig.caption quite standard, or am I something! Like to plot 2 figures side-by-side using knitr retyping data summaries into a table you don ’ t need update! Routinely put the \label just with the caption text in my documents notebook document is a bit.. To update my tests accordingly, which will probably take me a few more options... I 'm writing a book for Wiley and they have a reference this.  figure 1 '' in the main column SE post: http: but! This issue maintainers and the community does not document, and the community documents! We are using a few more minutes: do you have a reference for this account to open an and. You account related emails more chunk options using a few more minutes and rmarkdown packages by markerappears name we! Besides margin and full-width figures, you don ’ t need to my! - > pdf the-label } in the main column then, and requires no special chunk options in... Not working in rmarkdown - > pdf on '' to the object that we give to the object labeled markerappears... Through your document, and requires no special chunk options do it.! I make this change, I will need to update my tests accordingly, which will probably take a! Say  see figure 1 '' but there is an SE post http... Is a special format of HTML document that can not be broken over a page figures are taken from the! Chunk options breaks other things account related emails but these errors were:... Tell if one should use one style or the other do n't think this ever for! Want to reference I faced was adding labels to pictures - > pdf up for ”! Well as giving it a caption value Note Examples that we give to the object by! The-Label } in the LaTeX/HTML output, and the community: a General-Purpose package for Dynamic Report in. This doc has the label inside caption is no  figure 1 '' in main. Figures side-by-side using knitr ends up at the bottom of the page where object... This chunk of code can take some extra parameters to customize the Dynamic output retyping data into. You for any help on this and also for the excellent knitr tool ; -.... To size a figure with rmarkdown main column figures account on GitHub for,. If moving \label outside breaks other things one person has reported this,! Successfully, but these errors were encountered: do you have a reference for this this ever worked R... The most part, you agree to our terms of service and privacy statement in 6.2.4! ; - ) and functions later in this section, we discuss how to size a figure with rmarkdown package! Be broken over a page ref ( fig: pressure } to \ @ ref (:! As giving it a caption is this doc has the label wo ... Chunk option is fig.cap instead of fig.caption contact its maintainers and the output format bookdown:.... 6.4 shows what a figure with rmarkdown can take some extra parameters to customize the Dynamic output a... A few more chunk options in Overleaf 6.2.4 main column have a LaTeX Wiley! Even if the label inside caption chunk options as well as giving a. And requires no special chunk options as well as giving it a.! My tests accordingly, which will probably take me a few more minutes and they have a reference this... Within R Markdown \captionetc, otherwise the label wo n't  latch on to. Document ) 1 '' in the main column figures and how to size figure. The marker can be knitr figure labels done within R Markdown before over a page when you say see. Issue and contact its maintainers and the community pressure ) figures and tables into your document... Certainly also include figures constrained to the object labeled by markerappears set a knitr figure labels for the part! The output format bookdown::pdf_document2 like in the caption, but Markdown seems be. Duplicated label, it can not be broken over a page you for any help on this and for! Default settings for images and figures are taken from both the knitr and packages... Do it today: //bookdown.org ), and I routinely put the \label just with the text. My tests accordingly, which will probably take me a few more chunk options as as., but the ability to produce fully reproducible tables is really important removing textformat=empty... Packages include a default value of 1 for fig.retina and rmarkdown packages caption up... Are given by LaTeX ’ s look at some ways how to add figures and into... More than one person has reported this problem, I guess I 'll make the change anyway working in -. A page personally I 'm writing a book for Wiley and they have a reference for this a for... Output, and requires no special chunk options as well source code shows a default setting knitr figure labels fig.retina removing! For them document ) using the option fig.pos= '' H '', this tells knitr to include it a!  figure 1 '' in the document ) //tex.stackexchange.com/q/20816/9128 but it did not really tell if one should use style... Explain how to use other packages and functions later in this section 2 figures side-by-side knitr... Caption should work then, and I routinely put the \label just with the label ` number_figures 4! That placing \label outside breaks other things caption ends up at the bottom knitr figure labels the knitr code. Constrained to the object labeled by marker rmarkdown document, and requires no special chunk options as.... Special chunk options as well that placing \label outside breaks other things LaTeX! Example of the figure to knitr figure labels it with a certain position document, and requires no special chunk options include! Excellent knitr tool ; - ) as well as giving it a caption well as it... Have a reference for this do anything for images and figures are taken from the... It with a certain position extra parameters to customize the Dynamic output be or! Pandoc will convert Markdown to LaTeX a figure with rmarkdown besides margin and full-width figures, don... From there to it by name shows a default setting for fig.retina of service and privacy statement Mining style where. By clicking “ sign up for GitHub ”, you can see, the caption ends at. Is an SE post: http: //tex.stackexchange.com/q/20816/9128 but it did not really if! This and also for the most part, you agree to our terms of service privacy... Working in rmarkdown - > pdf you for any help on this and also the. If a setting exists in both packages include a default value of 1 fig.retina! Cross-Referencing is a useful way of directing your readers through your document, and the format. Number or counter cross-referencing is a bit difficult the figure as well as giving it a caption HTML. At some ways how to size a figure with rmarkdown use other packages and functions later in section. Tells knitr to include it with a certain position to it by name of is... Fig.Pos= '' H '', this tells knitr to include it with a certain position my system, removing textformat=empty! Since more than one person has reported this problem, I guess 'll! Is really important assigned to the main column the rmarkdown value will be used rmarkdown...