I am looking to render a 2 column report as a stand-alone HTML file using R and Markdown only. I am very new to markdown within R, so I need some help with the layout.
The image below displays the layout of what I would like to render using RMarkdown.
The HTML is on the left hand side and some data along the right hand side.
The raw HTML and the example dataframe can be found here:
Note: I used the pander package to create the table using the following command:
pandoc.table(df, style="rmarkdown")
Although this is not a perfect solution, it is a place to get started: Yihui recently added HTML templates to knitr, and docco is a example two-column page: http://cran.r-project.org/web/packages/knitr/vignettes/docco-classic.html .
You can see the template file used for that output here: https://github.com/yihui/knitr/blob/master/inst/misc/docco-template.html.
Alternatively, you can try placing inline HTML right in your R Markdown chunks, but this is terribly hacky and you might feel like a bad person for doing it. We use results='asis' so that the cated HTML is rendered properly, and out.extra='' to ensure that the HTML used to generate the figures is generated right away, rather than the Markdown language for image inclusion.
```{r two-column, results='asis', echo=FALSE, out.extra=''}
library(knitr)
cat("<table class='container'><tr>")
cat("<td>")
plot( rnorm(10) )
cat("</td>")
cat("<td>")
kable( rnorm(10), format="html" )
cat("</td>")
cat("</tr></table>")
```
Calling knit on that should produce a 2 column layout for that particular chunk (although without any nice styling for the table; you might add that in yourself with some CSS)
Related
I am searching for a way to produce a standalone HTML document from a chunk in Rmarkdown.
My example is this:
I have an Rmarkdown document for my analysis.
In one chunk of code, I produce interactive plotly plots that are quit long to load when I open the HTML.
I am looking for an option that would create another HTML document for this particular chunk and put a link to it in its place in the master HTML document.
I am sure I could manage to do something like that with a bit of tweaking with another script, but I would like to know if there is not a simpler option first.
Thanks
Yes, you can nest documents using knitr child documents. Put the chunk you want to isolate in its own Rmd (say, child.Rmd), then use this syntax to insert it in the master document:
```{r child='child.Rmd'}
```
I am trying to insert a pdf image into an r markdown file. I know it is possible to insert jpg or png images. I was just wondering if it is also possible to insert a pdf image. Thanks very much!
If you are just trying to insert an image that has been exported from, for example, some R analysis into a pdf image, you can also use the standard image options from the knitr engine.
With something like:
```{r, out.width="0.3\\linewidth", include=TRUE, fig.align="center", fig.cap=c("your caption"), echo=FALSE}
knitr::include_graphics("./images/imagename.pdf")
```
Unfortunately you can't specify the initial dimensions of your image output (fig.width and fig.height), which you would need to pre-define in your initial output, but you can specify the ultimate size of the image in your document (out.width). As noted below, however, this is limited to scaling down.
You could also of course leave out the initial directory specification if your files are in the same working directory. Just be aware of operating system differences in specifying the path to the image.
An alternative method is to use Markdown syntax noted by #hermestrismegistus on this post:
{width=65%}
This can also be collected for multiple images side-by side:
{width=33%}{width=33%}{width=33%}
Edit:
After working more extensively with in-text referencing, I have found that using r chunks and the include_graphics option to be most useful. Also because of the flexibility in terms of image alignment (justification).
As an example:
```{r image-ref-for-in-text, echo = FALSE, message=FALSE, fig.align='center', fig.cap='Some cool caption', out.width='0.75\\linewidth', fig.pos='H'}
knitr::include_graphics("./folder/folder/plot_file_name.pdf")
```
The reference can later be used in-text, for example, Figure \#ref(fig:image-ref-for-in-text) illustrates blah blah.
Some important things to note using this format:
You can only expand PDF images via a code chunk up to the out.width and out.height conditions set in the original .pdf file. So I would recommend setting them slightly on the larger side in your original image (just note that any chart text will scale accordingly).
The in-text reference code (in this case image-ref-for-in-text) CANNOT contain any underscores (_) but can contain dashes (-). You will know if you get this wrong by an error message stating ! Package caption Error: \caption outside float.
To stop your plots drifting to the wrong sections of your document, but in a way that unfortunately will generate some white space, the above example includes fig.pos='H'. Where H refers to "hold" position. The same can be achieved for the former Markdown option by placing a full-stop (period .) immediately after the last curly bracket.
Example:
{width=75%}.
Unfortunately, this latter option results in some unsightly full-stops. Another reason I prefer the include_graphics option.
Sorry, I found that there is a similar post before:
Add pdf file in Rmarkdown file
Basically, I can use something like below works well for the html output:
<img src="myFirstAlignment2.pdf" alt="some text" width="4200" height="4200">
And something like below works well for the pdf output:
(1)possible solution
\begin{center} <br>
\includegraphics[width=8in]{myFirstAlignment2.pdf} <br>
\end{center}
(2)possible solution
The myFirstAlignment2.pdf should be replaced with path\myFirstAlignment2.pdf if the pdf file is not in your working directory.
In relation to the comment of the best answer, there is a way to use the second option, and the output not come out tiny.
Use the following syntax below with the height being a large number. Having text in the brackets is necessary for it to work.
{width=100% height=400}
None of the answers outlined worked well for me in terms of sizing the pdf, so adding another answer using the code chunk options for out.height and out.width to control the size:
```{r out.height = "460px", out.width='800px', echo=F}
knitr::include_graphics("./images/imagename.pdf")
```
I was looking for a way to change the setting in my Rmd file so that the html output contains all the columns and the table does not break. I tried to change the css properties as in this solution (Output table width in Rmarkdown) but this does not affect my output.
I have currently 17 columns and using a pandoc.table, but only 5 coloumns are shown before the table is broken and the next 5 columns are displayed below.
What changes do I need to make so that the entire table can be shown in my html output?
Thanks for your help.
I can't use the pandoc package because is not currently available for R version 3.2.0. Instead, I used knitr with the kable() function. This code works fine:
{r, echo=FALSE, results='asis'}
library(knitr)
examp <- data.frame(matrix(rep("Unicorn"), nrow=5, ncol=100))
kable(examp)
I think, because you don't provide an example, that you need to specify the results='asis' chunk option.
Try ?kable for further information.
Anyway ?pandoc.table shows that there is an option split.table that may help.
I want to center an image and/or text using R Markdown and knit a PDF report out of it.
I have tried using:
->Text<-
-><-
That does not do the trick! Any other way of getting this done?
I had the same question. I have tried all solutions provided above and none of them worked... But I have found a solution that works for me, and hopefully for others too.
<center>
</center>
This code will center both the image and the caption. It is essential that you leave lines between <center>, the image code, and </center>, otherwise the image will be centered but the caption will disappear.
If you want your image to have a clickable link, you can embed things like
[](www.link_to_image.com)
However, the caption will no longer appear.
So if you want a clickable caption you will have to do it in two steps:
<center>
[your image caption](www.link_to_image.com)
</center>
Same here, make sure there are empty lines in between each command ones. If you want both the image and the caption to be clickable, then combine the middle and the last codes above. I hope this helps a bit.
If you are centering the output of an R code chunk, e.g., a plot, then you can use the fig.align option in knitr.
```{r fig.align="center"}
plot(mtcars)
```
You can use raw LaTeX in R Markdown. Try this:
\begin{center}
Text
\end{center}
There is, of course, a catch: everything between begin{...} and \end{...} is interpreted as raw LaTeX by Pandoc, so you can't use this technique to center the output of R code chunks, or Markdown content.
You can set the center (or other) alignment for the whole document as a Knitr option, using:
knitr::opts_chunk$set(echo = TRUE, fig.align="center")
None of the answers work for all output types the same way and others focus on figures plottet within the code chunk and not external images.
The include_graphics() function provides an easy solution. The only argument is the name of the file (with the relative path if it's in a subfolder). By setting echo to FALSE and fig.align=center you get the wished result.
```{r, echo=FALSE, fig.align='center'}
include_graphics("image.jpg")
```
I used the answer from Jonathan to google inserting images into LaTeX and if you would like to insert an image named image1.jpg and have it centered, your code might look like this in Rmarkdown
\begin{center}
\includegraphics{image1}
\end{center}
Keep in mind that LaTex is not asking for the file exention (.jpg). This question helped me get my answer. Thanks.
The simple solution given by Jonathan works with a modification to cheat Pandoc. Instead of direct Latex commands such as
\begin{center}
Text
\end{center}
you can define your own commands in the YAML header:
header-includes:
- \newcommand{\bcenter}{\begin{center}}
- \newcommand{\ecenter}{\end{center}}
And then you use:
\bcenter
Text and more
\ecenter
This works for me for centering a whole document with many code chunks and markdown commands in between.
I'm using beamer to knit pdf from Rmarkdown and what worked for me is:
\centering
If you know your format is PDF, then I don't see how the HTML tag
can be useful... It definitely does not seem to work for me. The other pure LaTeX solutions obviously work just fine. But the whole point of Markdown is not to do LaTeX but to allow for multiple format compilation I believe, including HTML.
Therefore, with this in mind, what works for me is a variation of Nicolas Hamilton's answer to Color Text Stackoverflow question:
#############
## CENTER TXT
ctrFmt = function(x){
if(out_type == 'latex' || out_type == 'beamer')
paste0("\\begin{center}\n", x, "\n\\end{center}")
else if(out_type == 'html')
paste0("<center>\n", x, "\n</center>")
else
x
}
I put this inside my initial setup chunk.
Then I use it very easily in my .rmd file:
`r ctrFmt("Centered text in html and pdf!")`
There is now a much better solution, a lot more elegant, based on fenced div, which have been implemented in pandoc, as explained here:
::: {.center data-latex=""}
Some text here...
:::
All you need to do is to change your css file accordingly. The following chunk for instance does the job:
```{cat, engine.opts = list(file = "style.css")}
.center {
text-align: center;
}
```
(Obviously, you can also directly type the content of the chunk into your .css file...).
The tex file includes the proper centering commands.
The crucial advantage of this method is that it allows writing markdown code inside the block.
In my previous answer, r ctrFmt("Centered **text** in html and pdf!") does not bold for the word "text", but it would if inside a fenced div.
For images, etc... the lua filter is available here
Just to update the question. To do this some easy way, you can add fig.align="center" to the chunk with the chuck knitr options:
knitr::opts_chunk$set(echo = TRUE,
fig.align="center" #align all the figures in the center
)
none of the answers worked but this
\newcommand{\bcenter}{\begin{center}}
\newcommand{\ecenter}{\end{center}}
but then the following problem is that it works for only one figure and then will not for any other figures.
I just started learning R I knew it was going to be difficult but what's worst is that there is little to no info that I can refer to.
None of these solutions worked for me when inserting a pdf figure in the text. After intensive trial and error, what made the trick for me (for a pdf output) was:
\hfil  \hfil
Since the question asks for both text and image alignment and I had a hard time finding an option for text that worked, with non of the ones above working withing a code chunk (for me). I wanted to share this: it seem to do the trick to the best of it's abilities (meaning it's not perfectly centered but close)
centerText <- function() {
width <- getOption("width")
out <- "your text"
ws <- rep(" ", floor((width - nchar(out))/2))
cat(ws, out, sep = "")
}
centerText()
Original code comes from here
I'm trying to come up with a good system for generating slides and accompanying handouts. The ideal system would have the following properties:
beautiful in both presentation (PDF/HTML) and handout (PDF) layouts (handouts should have room for taking notes)
embedded R chunks, figures, other JPG/PNG pictures, etc.
easy to compose
build using command-line tools
bibliography support
pandoc slide separator format (automatically generate a new slide after headers of a specified level) is preferred
I can live with a little bit of additional processing (e.g. via sed), but would prefer not to write a huge infrastructure
two-column layouts: there is a SO post on how to get multi-column slides from pandoc, but it is LaTeX- rather than HTML-oriented.
ability to adjust sizes of embedded images (other than R-generated figures) and column widths on the fly
Here's what I've discovered so far about the various options:
Slidify:
doesn't do pandoc slide separator format, although there is a workaround
the suggestion for creating handouts is to print to PDF; I'd like to leave room for notes etc. (I could probably figure out a way to do that using something like PDFtk or psnup ...)
RStudio presentations (.Rpres files):
does lots of things nicely, including multi-columns with specified widths
doesn't support pandoc slide separator format
I can't figure out what's going on under the hood. There is RStudio documentation that describes the translation process for regular HTML, but it doesn't seem to cover the R presentation format (which isn't quite the same). (I have previously invested some effort in figuring out how to get RStudio-like output via pandoc ...), which means I can't generate slides etc. from the command line.
RStudio's Development Version (as of March 2014) comes bundled with Pandoc and version 2 of rmarkdown. It addresses many of the above issues with the .Rpres format.
pandoc: may be the only markdown-translator that has features such as footnotes, bibliography support, etc.. I can also use pandoc to generate LaTeX using the tufte-handout class, which meets my criteria of beauty.
Unfortunately, it seems not to have built-in two-column format support. Yihui Xie's HTML5 example doesn't show any two-column examples, and it claims (on slide 5) that clicking the "Knit HTML" button in RStudio is equivalent to pandoc -s -S -i -t dzslides --mathjax knitr-slides.md -o knitr-slides.html, but it doesn't seem to be ...
LaTeX/beamer: I could simply compose in Rnw (knitr-dialect Sweave) rather than R markdown to begin with. This would give me ultimate flexibility ...
despite many years of LaTeX use I do find LaTeX composition more of a pain than markdown composition.
After all that, my specific question is: what's the best (easiest) way to generate a two-column layout for HTML output?
Any other advice will also be appreciated.
This is an old Q, but I was recently plagued by a similar question, here's what I found:
Using the RPres format, two columns can be specified like so (details). Note that RPres can only be converted to HTML by clicking a button in RStudio, there doesn't seem to be any command line method, which is a bit annoying. Despite, that I'd say it is currently the simplest and most flexible method for getting slide columns with markdown:
===
Two Column Layout
===
This slide has two columns
***
```{r, echo=FALSE}
plot(cars)
```
Some flexibility is afforded by adjusting the column proportions:
===
Two Column Layout
===
left: 30%
This slide has two columns
***
```{r, echo=FALSE}
plot(cars)
```
With rmarkdown we can get two columns, but with no control over where the break is, which is a bit of a problem:
---
output: ioslides_presentation
---
## Two Column Layout {.columns-2}
This slide has two columns
```{r, echo=FALSE}
plot(cars)
```
We can also mix markdown and LaTeX in an Rmd file using the beamer_presentation format in RStudio to get two columns like this, but can't run any code in either column, which is a limitation:
---
output: beamer_presentation
---
Two Column Layout
-------
\begin{columns}
\begin{column}{0.48\textwidth}
This slide has two columns
\end{column}
\begin{column}{0.48\textwidth}
If I put any code in here I get an error, see
https://support.rstudio.com/hc/communities/public/questions/202717656-Can-we-have-columns-in-rmarkdown-beamer-presentations-
\end{column}
\end{columns}
Seems like a regular Rnw LaTeX doc is the best way to get columns if you want to use LaTex, not this markdown hybrid (cf. two column beamer/sweave slide with grid graphic)
In all of the above an image can be placed in an column.
The slidify website has instructions on making two columns here: http://slidify.org/customize.html but it's not clear what has to go into the assets/layouts folder to make it work
You can use fenced_divs notation or ::: to create columns or `Two Content layout'. See also this page to know more about the notation.
## Slide With Image Left
::: columns
:::: column
left
::::
:::: column
right
```{r your-chunk-name, echo=FALSE, fig.cap="your-caption-name"}
knitr::include_graphics("your/figure/path/to/the-image.pdf")
#The figure will appear on the right side of the slide...
```
::::
:::
Since pandoc 2+, which supports the notation, was implemented in RStudio v1.2+, you may need to install RStudio v1.2+ first. The installation is easy enough (at least in my case); just download and install RStudio v1.2+. In the way of installation, the former version of RStudio on your computer will be replaced with the new one without uninstalling it manually.
The ::: notation can be used even when you knit .Rmd files with beamer_presentation option, as well as when you create HTML slides. So we don't have to neither mix markdown and LaTeX notation in one file, nor add additional codes any longer: just knit the file as you knit other .Rmd with other options.
I now have what I think is a reasonable solution that should apply at least to ioslides-based solutions, and maybe (?) to other HTML5-based formats. Starting here, I added
<style>
div#before-column p.forceBreak {
break-before: column;
}
div#after-column p.forceBreak {
break-after: column;
}
</style>
to the beginning of my document; then putting <p class="forceBreak"></p> within a slide with {.columns-2} breaks the column at that point, e.g.
## Latin hypercube sampling {.columns-2}
- sample evenly, randomly across (potentially many) uncertain parameters
<p class="forceBreak"></p>
[User:Saittam, Wikipedia](https://commons.wikimedia.org/wiki/File:LHSsampling.png#/media/File:LHSsampling.png)
There may be an even better way, but this isn't too painful.
#ChrisMerkord points out in comments that
.forceBreak { -webkit-column-break-after: always; break-after: column; }
worked instead (I haven't tested ...)
I got an idea from HERE, the basic solutions was:
### Function *inner_join*
. . .
`<div style="float: left; width: 50%;">`
``` {r, echo = FALSE, results = 'markup', eval = TRUE}
kable(cbind(A,B))
```
`</div>`
`<div style="float: right; width: 50%;">`
```{r, echo = TRUE, results = 'markup', eval = TRUE}
inner_join(A,B, by="C")
```
`</div>`
There is a workaround for beamer error.
In short: Error is related to pandoc conversion engine, which treats everything between \begin{...} and \end{...} as TeX. It can be avoided by giving new definition for begin{column} and end{column} in yaml header.
Create mystyle.tex and write there:
\def\begincols{\begin{columns}}
\def\begincol{\begin{column}}
\def\endcol{\end{column}}
\def\endcols{\end{columns}}
In the Rmd file use these new definitions
---
output:
beamer_presentation:
includes:
in_header: mystyle.tex
---
Two Column Layout
-------
\begincols
\begincol{.48\textwidth}
This slide has two columns.
\endcol
\begincol{.48\textwidth}
```{r}
#No error here i can run any r code
plot(cars)
```
\endcol
\endcols
And you get:
So far I haven't been able to do better than hacking my own little bit of markup on top of the rmd format: I call my source file rmd0 and run a script including this sed tidbit to translate it to rmd before calling knit:
sed -e 's/BEGIN2COLS\(.*\)/<table><tr><td style="vertical-align:top; width=50%" \1>/' \
-e 's/SWITCH2COLS/<\/td><td style="vertical-align:top">/' \
-e 's/END2COLS/<\/td><\/tr><\/table>/' ...
There are a few reasons I don't like this. (1) It's ugly and special-purpose, and I don't have a particularly good way to allow optional arguments (e.g. relative widths of columns, alignment, etc.). (2) It has to be tweaked for each output format (e.g. if I wanted LaTeX/beamer output I would need to substitute \begin{columns}\begin{column}{5cm} ... \end{column}\begin{column}{5cm} ... \end{column}\end{columns} instead (as it turns out I want to ignore the two-column formatting when I make LaTeX-format handouts, so it's a little easier, but it's still ugly).
Slidify may yet be the answer.
Not a direct solution, but Yihui's Xaringan package https://github.com/yihui/xaringan/ works for me. It's based on remark.js. In the default template, you can use .pull-left[] and .pull-right[] . Example: https://slides.yihui.name/xaringan/#15. You only need a minimum tweak on the existing .rmd files.