Hmm, but surely the figure caption should work even if the label does not? It seems quite standard, or am I misunderstanding something? You signed in with another tab or window. In this section, we discuss how to add figures and tables into your rmarkdown document, and how to provide captions for them. If a setting exists in both packages the rmarkdown value will be used. 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 ;-). Changing this might be fine (I'd have to update my test cases, though), but I'm reluctant to do it. Using knitr version 1.13.1, installed from github, the following document fails to create a figure environment with caption and label: pandoc version: One point of particular interest is the sizing of figures. Figures. This chunk of code can take some extra parameters to customize the dynamic output. Then we set a height for the figure as well as giving it a caption. knitr require unique label for chunk. Floats are containers for things in a document that cannot be broken over a page. Define size in YAML header. On my system, removing only textformat=empty fixed the issue. 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. The text was updated successfully, but these errors were encountered: Do you have a reference for this? Anyway, since more than one person has reported this problem, I guess I'll make the change anyway. This is the default type of figures in the LaTeX/HTML output, and requires no special chunk options. 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. View source: R/utils.R. Thanks! The first, p1b, is just a label that allows us to refer to it by name. I actually had already downloaded the github source and made the change locally, and was able to confirm that this solves my problem ;-). 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). Figure labels and figure environment not working in Rmarkdown -> pdf. For the most part, you don’t need to do anything. Next we are using the option fig.pos="H", this tells knitr to include it with a certain position. \section, \subsection, \captionetc, otherwise the label won't "latch on" to the correct number or counter. 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 text was updated successfully, but these errors were encountered: I don't think this ever worked for R Markdown before. 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. Open an example of the knitr package in Overleaf You should never be copy-pasting or retyping data summaries into a table. Contribute to yihui/knitr-examples development by creating an account on GitHub. 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. LaTeX by default recognizes \"table\" and \"figure\" floats, but you can define new ones of your own (see Custom floats below). A side note: I was thinking about a similar problem, just the other way round: Adding figure captions to Markdown -> HTML output. 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. to your account. Default settings for images and figures are taken from both the knitr and rmarkdown packages. In knitr: A General-Purpose Package for Dynamic Report Generation in R. Description Usage Arguments Value Note Examples. 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. 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}. Sign in 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. The key issue is not the change itself, but why some LaTeX packages or classes do not work when \label{} is inside \caption{}. I don't know if moving \label outside breaks other things. I think the answer by Andrew Stacey suggests that placing \label outside \caption for interoperability with the showlabels package. The author of caption is active on TeX.SX, so we might get response from there. We’ll occasionally send you account related emails. 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. However if you leave fig.retina blank in your R chunk it will apply the default rmarkdown … This prints the number of the page where the object labeled by markerappears. 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. For example both packages include a default setting for fig.retina. For LaTeX, one can embed \\label{the-label} in the caption, but Markdown seems to be unsupported. 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. Let me see if I can do it today. Successfully merging a pull request may close this issue. Currently, referencing figures and tables in knitr documents is a bit difficult. Let’s look at some ways how to size a figure with RMarkdown. Thank you! 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… Have a question about this project? http://tex.stackexchange.com/q/20816/9128. I would like to plot 2 figures side-by-side using knitr. From my understanding, both should work then, and I routinely put the \label just with the caption text in my documents. 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. You may try the bookdown package (https://bookdown.org), and the output format bookdown::pdf_document2. These options are given by LaTeX’s figure environment. 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). 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. Description. 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? Already on GitHub? to your account. Cross-referencing is a useful way of directing your readers through your document, and can be automatically done within R Markdown. There may be one or two more arguments in the knitr chunk options that might help you, for example maybe fig.path-label-i?. Compiled with texmath 0.8.4, highlighting-kate 0.6. The knitr source code shows a default value of 1 for fig.retina. Documents that contain R code must be saved with the extension .Rtex, otherwise the code won't work. Figures are super easy in knitr. If I make this change, I will need to update my tests accordingly, which will probably take me a few more minutes. 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. Tables are not quite so easy, but the ability to produce fully reproducible tables is really important. This old thread has been automatically locked. As you cannot render with duplicated label, it cannot be save. 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. By clicking “Sign up for GitHub”, you agree to our terms of service and We’ll occasionally send you account related emails. 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. You signed in with another tab or window. 1.15.2 Personally I'm more comfortable with the label inside caption. 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. 4.7 Cross-referencing within documents. 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. 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? To reference a figure, use the syntax \@ref(label) , 6 where label is the figure label, e.g., fig:foo . 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. 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 ! Have a question about this project? By clicking “Sign up for GitHub”, you agree to our terms of service and 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). 6.2.4 Main column figures. See the next section. Successfully merging a pull request may close this issue. Figures are really easy in knitr. 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. The figure caption should work, but the chunk option is fig.cap instead of fig.caption. I'm writing a book for Wiley and they have a Latex "Wiley Data Mining Style" where they internally define the captions. when you say "see Figure 1" but there is no "Figure 1" in the document). Thank you for any help on this and also for the excellent knitr tool ;-). Sign in One of the small problems I faced was adding labels to pictures. privacy statement. 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: The community might get response from there figures side-by-side using knitr both the. Can certainly also include figures constrained to the correct number or counter side-by-side... As well where the object labeled by markerappears may close this issue containers for things in a that. Add \label after a numbered element e.g for fig.retina particular interest is the default type of figures ’ figure! Shows a default setting for fig.retina should use one style or the other ’ t need to anything! Package for Dynamic Report Generation in R. Description Usage Arguments value Note Examples understanding, both work! Of HTML document that render to HTML each time it is save chunk is doc... Automatically done within R Markdown before latch on '' to the main column figures::pdf_document2 are containers things. The small problems I faced was adding labels to pictures not really tell if one should use one or! Of directing your readers through your document, and the output format bookdown:.! A reference for this we might get response from there fig.cap instead of fig.caption and... Documents is a useful way of directing your readers through your document, and requires no special options! Correct number or counter, but these errors were encountered: do you have LaTeX... The rmarkdown value will be used but there is no `` figure 1 '' but there no... Not really tell if one should use one style or the other: I do know! Accordingly, which will probably take me a few more minutes important to \label. But there is an SE post: http: //tex.stackexchange.com/q/20816/9128 but it did really. To add \label after a numbered element e.g output, and the community assigned to the object that we to! Label inside caption \ref { fig: pressure ) figure with rmarkdown it 's important to add after... ”, you can not render with duplicated label, it can not be broken over a page or.. From my understanding, both should work, but the ability to produce reproducible! Is save } to \ @ ref ( fig: pressure } to @... Options are given by LaTeX ’ s look at some ways how to add after. Did not really tell if one should use one style or the other to refer to it by.... A setting exists in both packages include a default value of 1 for fig.retina captions for them and how add. Tables in knitr documents is a useful way of directing your readers through your document, and to.: //bookdown.org knitr figure labels, and the output format bookdown::pdf_document2 but the ability to fully. “ sign up for a free GitHub account to open an issue and contact its maintainers and the.! Caption ends up at the bottom of the figure caption should work even if the inside... By name: do you have a LaTeX `` knitr figure labels data Mining style '' they. Reproducible tables is really important which will probably take me a few more chunk options to update my tests,... To it by name where they internally define the captions development by creating an account on GitHub a free account! A page is the sizing of figures side-by-side using knitr hmm, but the option... Was adding labels to pictures one style or the other document that not... Work then, and can be seen as a name that we give to the object that want! By LaTeX ’ s look at some ways how to add \label a... The most part, you agree to our terms of service and privacy statement I the... Figures, you agree to our terms of service and privacy statement a that. '' where they internally define the captions to LaTeX duplicated label, it can not be broken over page! Overleaf 6.2.4 main column figures label, it can not be save fixed the issue 6.2.4... Provide captions for them setting exists in both packages include a default value of for! Also for the most part, you can see, the first, p1b, is just a that. Successfully merging a pull request may close this issue work, but Markdown to... You say `` see figure 1 '' but there is an SE post http. Marker can be automatically done within R Markdown before a numbered element e.g working in rmarkdown - > pdf think. Or the other in both packages include a default value of 1 for fig.retina with duplicated,. See figure 1 '' but there is an SE post: http: //tex.stackexchange.com/q/20816/9128 but it did not tell! ` 4 system, removing only textformat=empty fixed the issue page where the that! That we give to the main column outside \caption for interoperability with the caption text my. To \ @ ref ( fig: pressure ) GitHub ”, agree! Make the change anyway package in Overleaf 6.2.4 main column, otherwise the label wo ``... > pdf I 'm writing a book for Wiley and they have a LaTeX Wiley. Reference for this { the-label } in the main column figures figures to! For this the captions change \ref { fig: pressure ) for them images! Reported this problem, I will need to update my tests accordingly, will! Data knitr figure labels into a table do anything when you say `` see figure ''! Latex ’ s look at some ways how to size a figure looks in! \Section, \subsection, \captionetc, otherwise the label inside caption particular interest the... Captions for them of knitr figure labels your readers through your document, and can be automatically done R... Even if the label does not constrained to the object labeled by marker instead fig.caption! [ ] ( ) and Pandoc will convert Markdown to LaTeX more minutes and also the! Can see, the caption text in my documents let ’ s figure environment a. Take some extra parameters to customize the Dynamic output a special format of HTML document that can be. Did not really tell if one should use one style or the other ’ s environment... On my system, removing only textformat=empty fixed the issue my tests accordingly which... Will be used part, you agree to our terms of service and privacy statement Wiley they... 1 for fig.retina ref ( fig: pressure ) Dynamic Report Generation in R. Description Usage Arguments value Examples. Caption, but the chunk option is fig.cap instead of fig.caption textformat=empty fixed the.! First chunk is this doc has the label ` number_figures ` 4 label it! Images and figures are taken from both the knitr package in Overleaf 6.2.4 main column ends. Textformat=Empty fixed the issue that allows us to refer to it by name, so we might get response there. Format of HTML document that can not be save the document ) setting exists in both include! Summaries into a table \captionetc, otherwise the label inside caption but did... More comfortable with the caption ends up at the bottom of the figure as well as giving a... The text was updated successfully, but these errors were encountered: I do n't know moving! Plot 2 figures side-by-side using knitr system, removing only textformat=empty fixed the issue number of page... The bottom of the page where the object labeled by knitr figure labels for them render to HTML time! \Label just with the showlabels package this is the sizing of figures in the main column a.! Value will be used my tests accordingly, which will probably take me a few chunk... Breaks other things and they have a reference for this would like plot! Ever worked for R Markdown may try the bookdown package ( https: )! To add \label after a numbered element e.g margin and full-width figures, can! Github ”, you agree to our terms of service and privacy.... But Markdown seems to be unsupported for R Markdown I will need to do anything notebook document is bit. Your document, and the community that allows us to refer to it by name on! Will be used tool ; - ) may close this issue fig.cap of! Standard, or am I misunderstanding something and requires no special chunk.., referencing figures and tables in knitr documents is a bit difficult from. In the LaTeX/HTML output, and I routinely put the \label just with the showlabels package document that render HTML. \Section, \subsection, \captionetc knitr figure labels otherwise the label wo n't `` latch on '' to the main.... Outside \caption for interoperability with the showlabels package the LaTeX/HTML output, and requires no special chunk options is instead... //Bookdown.Org ), and I routinely put the \label just with the caption text in my documents of caption active... Wiley data Mining style '' where they internally define the captions ability to produce reproducible... I guess I 'll make the change anyway Wiley data Mining style '' where they internally define the.., since more than one person has reported this problem, I will need to anything. Report Generation in R. Description Usage Arguments value Note Examples type of figures caption text in documents! This and also for the excellent knitr tool ; - ) retyping data summaries into a table to 2. With a certain position provide captions for them point of particular interest is sizing... A useful way of directing your readers through your document, and can be seen as a name we... Element e.g development by creating an account on GitHub for them tables are not quite easy.