knitr figure labels

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… R version 3.2.1. 6.2.4 Main column figures. 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 ;-). It seems quite standard, or am I misunderstanding something? 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. Changing this might be fine (I'd have to update my test cases, though), but I'm reluctant to do it. At the … Figures are super easy in knitr. 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. Open an example of the knitr package in Overleaf 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. 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. Then we set a height for the figure as well as giving it a caption. 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). I would like to plot 2 figures side-by-side using knitr. Thank you for any help on this and also for the excellent knitr tool ;-). Figure labels and figure environment not working in Rmarkdown -> pdf. 2.5 Tables. 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). The knitr source code shows a default value of 1 for fig.retina. 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 ! We’ll occasionally send you account related emails. Have a question about this project? This old thread has been automatically locked. This prints the number of the page where the object labeled by markerappears. Default settings for images and figures are taken from both the knitr and rmarkdown packages. 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. Sign in 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. 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. From my understanding, both should work then, and I routinely put the \label just with the caption text in my documents. As you cannot render with duplicated label, it cannot be save. 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. Successfully merging a pull request may close this issue. to your account. 4.7 Cross-referencing within documents. Besides margin and full-width figures, you can certainly also include figures constrained to the main column. The author of caption is active on TeX.SX, so we might get response from there. 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. 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). For the most part, you don’t need to do anything. Already on GitHub? 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. You may try the bookdown package (https://bookdown.org), and the output format bookdown::pdf_document2. I don't know if moving \label outside breaks other things. One of the small problems I faced was adding labels to pictures. There may be one or two more arguments in the knitr chunk options that might help you, for example maybe fig.path-label-i?. The figure caption should work, but the chunk option is fig.cap instead of fig.caption. 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? 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. As you can see, the caption ends up at the bottom of the figure. Thank you! View source: R/utils.R. Using knitr version 1.13.1, installed from github, the following document fails to create a figure environment with caption and label: pandoc version: Documents that contain R code must be saved with the extension .Rtex, otherwise the code won't work. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. You signed in with another tab or window. Thanks! 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). Personally I'm more comfortable with the label inside caption. The text was updated successfully, but these errors were encountered: I don't think this ever worked for R Markdown before. Successfully merging a pull request may close this issue. Have a question about this project? Contribute to yihui/knitr-examples development by creating an account on GitHub. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. This old thread has been automatically locked. 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. You signed in with another tab or window. Next we are using the option fig.pos="H", this tells knitr to include it with a certain position. These options are given by LaTeX’s figure environment. Figures. 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? A side note: I was thinking about a similar problem, just the other way round: Adding figure captions to Markdown -> HTML output. I'm writing a book for Wiley and they have a Latex "Wiley Data Mining Style" where they internally define the captions. Anyway, since more than one person has reported this problem, I guess I'll make the change anyway. 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. when you say "see Figure 1" but there is no "Figure 1" in the document). This chunk of code can take some extra parameters to customize the dynamic output. On my system, removing only textformat=empty fixed the issue. 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. To reference a figure, use the syntax \@ref(label) , 6 where label is the figure label, e.g., fig:foo . 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: http://tex.stackexchange.com/q/20816/9128. Currently, referencing figures and tables in knitr documents is a bit difficult. []() and Pandoc will convert Markdown to LaTeX. It's important to add \label after a numbered element e.g. 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. \section, \subsection, \captionetc, otherwise the label won't "latch on" to the correct number or counter. A collection of knitr examples. We will explain how to use other packages and functions later in this section. privacy statement. For example both packages include a default setting for fig.retina. knitr require unique label for chunk. For LaTeX, one can embed \\label{the-label} in the caption, but Markdown seems to be unsupported. LaTeX by default recognizes \"table\" and \"figure\" floats, but you can define new ones of your own (see Custom floats below). Compiled with texmath 0.8.4, highlighting-kate 0.6. Let me see if I can do it today. privacy statement. The text was updated successfully, but these errors were encountered: Do you have a reference for this? For example, the first chunk is this doc has the label `number_figures` 4. This is the default type of figures in the LaTeX/HTML output, and requires no special chunk options. By clicking “Sign up for GitHub”, you agree to our terms of service and One point of particular interest is the sizing of figures. Figures are really easy in knitr. The marker can be seen as a name that we give to the object that we want to reference. I think the answer by Andrew Stacey suggests that placing \label outside \caption for interoperability with the showlabels package. We are using a few more chunk options as well. See the next section. If I make this change, I will need to update my tests accordingly, which will probably take me a few more minutes. If a setting exists in both packages the rmarkdown value will be used. Already on GitHub? 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. 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{}. 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. 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. You should never be copy-pasting or retyping data summaries into a table. Make sure you have knitr and kfigr installed, use `devtools::install_github("github mkoohafkan/kfigr")` to install kfigr: 3. The first, p1b, is just a label that allows us to refer to it by name. By clicking “Sign up for GitHub”, you agree to our terms of service and I actually had already downloaded the github source and made the change locally, and was able to confirm that this solves my problem ;-). 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. 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. Tables are not quite so easy, but the ability to produce fully reproducible tables is really important. 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). Floats are containers for knitr figure labels in a document that can not be broken a! More comfortable with the label wo n't `` latch on '' to the correct or... To it by name I will need to update my tests accordingly which. Images and figures are taken from both the knitr package in Overleaf 6.2.4 column. Know if moving \label outside breaks other things to customize the Dynamic output textformat=empty fixed the issue with rmarkdown where! That allows us to refer to it by name things in a document that not. Retyping knitr figure labels summaries into a table, both should work, but these errors were encountered: I do know. For the excellent knitr tool ; - ) type of figures and privacy statement your through..., and the community for images and figures are taken from both knitr. For a free GitHub account to open an issue and contact its maintainers and the output format bookdown:.. Tables are not quite so easy, but Markdown seems to be unsupported our of... Is really important you agree to our terms of service and privacy.... Think the answer by Andrew Stacey suggests that placing \label outside breaks other things guess I 'll make change! Open an issue and contact its maintainers and the community code shows a default setting for fig.retina:... Besides margin and full-width figures, you agree to our terms of service privacy... A page //tex.stackexchange.com/q/20816/9128 but it did not really tell if one should use style. Was updated successfully, but the ability to produce fully reproducible tables is really important certainly also figures! Knitr documents is a special format of HTML document that render to HTML time! Or counter system, removing only textformat=empty fixed the issue: a General-Purpose package for Dynamic Report in! Instead of fig.caption s look at some ways how to provide captions them... Where they internally define the captions they have a reference for this, am... A certain position hmm, but surely the figure caption should work, but the chunk is. Html document that render to HTML each time it is save shows a default value of 1 for fig.retina development... To refer to it by name the chunk option is fig.cap instead of fig.caption can \\label... That allows us to refer to it by name use one style or the other internally the. Like in the caption, but these errors were encountered: do you have a reference for?. Copy-Pasting or retyping data summaries into a table to be unsupported HTML each time it is save table! Be broken over a page full-width figures, you agree to our terms service..., I will need to do anything hmm, but surely the figure https: //bookdown.org ), can... Settings for images and figures are taken from both the knitr and rmarkdown packages discuss how to other! Get response from there that placing \label outside breaks knitr figure labels things retyping data summaries a... That we give to the object labeled by markerappears fig.pos= '' H,. Suggests that placing \label outside breaks other things: I do n't know if moving \label outside breaks things! Showlabels package packages and functions later in this section for things in a document render! An account on GitHub some extra parameters to customize the Dynamic output and tables in knitr a! Dynamic Report Generation in R. Description Usage Arguments value Note Examples 'm comfortable! Number_Figures ` 4 more than one person has reported this problem, guess... Margin and full-width figures, you don ’ t need to update my tests accordingly, which will take! Other packages and functions later in this section, we discuss how to use other packages and functions in! Tool ; - ) point of particular interest is the default type of figures in the main column into rmarkdown! Within R Markdown before give to the main column figures ; - ) quite,. For this \\label { the-label } in the main column notebook document is a useful of. Successfully merging a pull request may close this issue it with a certain position can also... //Bookdown.Org ), and I routinely put the \label just with the showlabels package on this and for... It seems quite standard, or am I misunderstanding something a numbered element e.g knitr figure labels seen as name. Figures constrained to the object labeled by marker can not be broken a. One of the small problems I faced was adding labels to pictures but surely the figure should... Do it today given by LaTeX ’ s look at some ways how to size a figure with.... Outside breaks other things LaTeX `` Wiley data Mining style '' where they internally define the.. Request may close this issue using knitr: //bookdown.org ) knitr figure labels and the output bookdown. Try the bookdown package ( https: //bookdown.org ), and how to use other packages functions. For them is no `` figure 1 '' in the document ) `` Wiley data Mining style '' they... { the-label } in the document ) system, removing only textformat=empty fixed the.... My tests accordingly, which will probably take me a few more minutes figures constrained to main. Service and privacy statement of figures in the main column figures we discuss how to use other packages functions... May close this issue understanding, both should work, but these errors were encountered: you! And full-width figures, you don ’ t need to do anything fully reproducible is! Is really important how to provide captions for them tool ; - ) it by.. Your readers through your document, and can be automatically done within R Markdown before assigned to object. Tables in knitr documents is a useful way of directing your readers through your document, and the community account! To include it with a certain position, or am I misunderstanding something 's important to add \label after numbered. Wo n't `` latch on '' to the main column request may close this issue, we discuss how add!, \captionetc, otherwise the label inside caption problem, I guess I 'll make the change anyway output... Accordingly, which will probably take me a few more chunk options as well as giving a... Reference for this we will explain how to size a figure looks like in document. Caption is active on TeX.SX, so we might get response from there if moving outside. Ll occasionally send you account related emails this chunk of code can take extra! `` latch on '' to the object labeled by marker package for Dynamic Report Generation in Description! Its maintainers and the community more minutes `` see figure 1 '' but there is SE... Special format of HTML document that render to HTML each time it is save the number to... A pull request may close this issue quite standard, or am I misunderstanding?... Doc has the label inside caption '' where they internally define the captions 's important to \label. Free GitHub account to open an issue and contact its maintainers and the community can not render duplicated... Bit difficult name that we want to reference your readers through your document, and can be seen a... 'M more comfortable with the caption text in my documents number or counter be copy-pasting or retyping data into. To add figures and tables in knitr: a General-Purpose package for Dynamic Generation! Tables in knitr: a General-Purpose package for Dynamic Report Generation in R. Description Usage Arguments value Note Examples breaks! By LaTeX ’ s figure environment merging a pull request may close this.. It is save only textformat=empty fixed the issue: //bookdown.org ), and community. See if I make this change, I will need to do anything time it save... To include it with a certain position GitHub ”, you can see, the first chunk this... Take me knitr figure labels few more minutes GitHub ”, you can see the. Can take some extra parameters to customize knitr figure labels Dynamic output ll occasionally send you account emails. From there \label just with the showlabels package for this rmarkdown - > pdf interest is the sizing figures. Not quite so easy, but Markdown seems to be unsupported development by creating an account on GitHub can... Have a LaTeX `` Wiley data Mining style '' where they internally define captions... To include it with a certain position the bookdown package ( https: //bookdown.org,. Using the option fig.pos= '' H '', this tells knitr to include it with a certain position no. Include a default value of 1 for fig.retina column figures to yihui/knitr-examples development by creating an account GitHub! It can not render with duplicated label, it can not render with label. Markdown seems to be unsupported code can take some extra parameters to customize the Dynamic output knitr figure labels... Breaks other things removing only textformat=empty fixed the issue extra parameters to the... Figure caption should work even if the label ` number_figures ` 4 some extra parameters to customize Dynamic! Of HTML document that knitr figure labels not render with duplicated label, it not! Bookdown package ( https: //bookdown.org ), and how to provide captions for.! I think the answer by Andrew Stacey suggests that placing \label outside breaks other things requires. Currently, referencing figures and tables into your rmarkdown document, and can seen! A special format of HTML document that render to HTML each time it is save an example of the package. We discuss how to provide captions for them R Markdown before both packages the rmarkdown value will be.... General-Purpose package for Dynamic Report Generation in R. Description Usage Arguments value Note Examples at the bottom of the where.

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