I'm seeing different behaviour in an R Markdown (Rmd) file depending on how I reference the image I'd like to embed in an HTML document. In the simple example below, the second image is embedded in the document, but the first (using the R chunk) is not.
---
title: "title"
output:
html_document:
mode: selfcontained
theme: null
---
```{r packages, echo=FALSE}
library(htmltools)
```
```{r imgTest, echo=FALSE}
img(src = "http://placehold.it/350x150")
```
<img src="http://placehold.it/350x150">
This is the output in the HTML (for the relevant bit):
<p><img src="http://placehold.it/350x150"/></p>
<p><img src="data:image/png;base64,iVBORw0KG<SNIPPED>"></p>
In summary, using the htmltools function img() within a code chunk does not embed the image but instead it remains a link.
For various reasons, I need the document to be truly self-contained (no links) and to also avoid raw HTML.
Can anyone explain why this is happening and offer a solution? I've tried a variety of chunk options without success so far.
Related
Is it possible to create multiple output formats from a Quarto/R Markdown document at once by specifying them in the YAML header?
My guess did not work:
---
title: Stacked Area chart with Annotations
format:
- html
- gfm
---
Try this way (and suppose file name is format_test.qmd)
format_test.qmd
---
title: "Untitled"
format:
html: default
gfm: default
---
## Quarto
Quarto enables you to weave together content and executable code
into a finished document. To learn more about Quarto
see <https://quarto.org>.
## Running Code
When you click the **Render** button a document will
be generated that includes both content and the output
of embedded code. You can embed code like this:
```{r}
1 + 1
```
Then from console run this following code to generate both html and github flavoured markdown (gfm) file at once.
# install.packages("quarto")
quarto::quarto_render("format_test.qmd", output_format = "all")
Or if you prefer using the terminal (or if you are a non R-useR) you can run the following command in the terminal,
quarto render format_test.qmd --to gfm,html
Be careful to specify multiple formats without putting any space in between i.e. type them as gfm,html.
And running the above command in the terminal does not require you to specify format yaml option in your document. So, for
format_test.qmd
---
title: "Untitled"
---
## Quarto
Quarto enables you to weave together content and executable code
into a finished document. To learn more about Quarto
see <https://quarto.org>.
quarto render format_test.qmd --to pdf,html,gfm
will generate three files in HTML, pdf, and markdown format.
The example below (i.e. saved as a file index.rmd ) has the same code chunk to display an image above and below the top level heading, but the image doesn't appear above the top level heading. This occurs if there is a file _output.yml with only this entry bookdown::gitbook: in the same directory.
That line seems to enforce a table of contents (which I want) and that appears to strip out anything (image or text) before the first top level heading by default (which I don't want) - so can this behaviour be modified?
---
site: bookdown::bookdown_site
---
```{r echo=FALSE, message=FALSE, warning=FALSE}
library(imager)
im <- load.image(system.file('extdata/Leonardo_Birds.jpg',package='imager'))
plot(im, axes=FALSE)
```
# R Markdown
```{r echo=FALSE, message=FALSE, warning=FALSE}
library(imager)
im <- load.image(system.file('extdata/Leonardo_Birds.jpg',package='imager'))
plot(im, axes=FALSE)
```
What follows is workaround to your Options 2 and 3, using Markdown and CSS to style images and HTML+CSS to style text; also, using base64 image (transparent gif) generator as an space separator between elements.
Beware of whitespaces! (at the end of each line - place two white spaces and hit ENTER)
Does one of these approaches/hacks work for you? If not, it would be better to delete the answer, it may be misleading to others.
---
title: |
{width=300px}|
|:-:|
{width=300px style="display: block; margin:0 auto"}
{width=300px height=90px align=left}
{width=300px height=90px align=center}
{width=300px height=90px align=right}
{width=150px}
R Markdown Title
<center>R Markdown Title</center>
<p style="text-align: right;">R Markdown Title</p>
{width=150px}
author: "Author Name"
date: "08/03/2020"
---
Using Markdown table to "style" images |-| (left-aligned), |:-:| (centered) and |-:| (right-aligned) will work well with simple RMarkdown outputs.
I realised that you have an image under # top level heading positioned at the very top of the page - with top:0px. causing image duplication and, possibly, hover problem:
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:0px;height:100px;" />
replace with:
{width=50px style="display: block; margin:0 auto;"}
and see what will happen.
---
title: |
{width=300px style="display: block; margin:0 auto;"}
{width=50px}
R Markdown Title
{width=50px}
output:
html_document: default
---
# I'm a top level heading {-}
{width=50px style="display: block; margin:0 auto;"}
Note, you need to replace the image with a local image if you want to show the image in the rstudio viewer.
The image will be visible in the html file created when you knit, if you open in a browser connected to the internet.
```{r echo=FALSE, message=FALSE, warning=FALSE}
plot(cars)
```
EDIT:
Let's try to find a common ground, A Minimal Book Example, github here.
Adjustments made in index.Rmd:
---
title: |
{height=300px}
author: "Author Name"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::gitbook
---
# Prerequisites
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:50px;height:300px;align:center;" />
This is a _sample_ book written in **Markdown**. You can use anything that Pandoc's Markdown supports, e.g., a math equation $a^2 + b^2 = c^2$.
index.Rmd output:
Adjustments made in Chapter: Introduction (01-intro.Rmd):
# Introduction {#intro}
{height=240px}
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:50px;height:300px;align:center;" />
You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \#ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \#ref(methods).
01-intro.Rmd output:
With this solution we are "masking" a top level heading (# Introduction) with .png image, which will appear in the Table of Content as text.
Disadvantage: besides the obvious hack, image width must be at least equal or wider than top level heading title.
Note: 3 options are provided here, and none of them are perfect. The perfect solution may rely on modifications to the bookdown package?
Option 1:
Use includes with before_body like this in your _output.yml file (suggested here):
bookdown::gitbook:
css: assets/style.css
includes:
before_body: assets/big-image.html
after_body: assets/footer.html
Disadvantages:
i) Requires making a html file just to insert an image.
ii) If using a web-based image, won't show in Rstudio viewer.
iii) If using a local image, path can get mixed up and won't show in online web html rendering
iv) Includes image at the top of each chapter of bookdown if using before_body: my_image.html. Alternative option in_header: my_image.html does not seem compatible with the sidebar index.
Option 2
Insert image via yaml in index.rmd, using the solution under Tip 3 Add a Logo in your title/header/footer at this blog post
---
title: |
My title
Disadvantages:
i) When you hover over the image, it displays a copy of the image in a slightly different location (Can this "Hover" behaviour be disabled?)
ii) If using a web-based image, won't show in Rstudio viewer.
iii) If using a local image, path can get mixed up and won't show in online web html rendering
Option 3
The code below borrowed from here (which you can place below the top level heading) presumably goes direct through the knitting process and inserts itself in the final html. The issue is that the image doesn't make room for itself and ends up over the first text. Is there some simple html/css to sort this out?
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:0px;height:100px;" />
Disadvantages:
i) Image doesn't make room for itself and ends up over the first text. You can get around this with a hack by coding extra space (trial and error) through the yaml title like this:
title: |
.
.
.
.
site: bookdown::bookdown_site
EDIT
This is superseded by Radovan's accepted answer.
This was the best answer, taking option 3 from my previous answer, and combining a code approach to making the relevant space from Radovan's answer.
You will still have problems if you want to include a title in the YAML (I don't need this, as my title is in the image).
Also, on first loading the page, it presents nicely, but image is not seen if you go to the top of the document using the table of contents (the inheader approach used by this bookdown shows a better behaviour, but appears at the top of every chapter, which is not desired).
---
title: |
{height=300px}
output:
html_document: default
---
# I'm a top level heading {-}
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:50px;height:300px;align:center;" />
Note, you need to replace the image with a local image if you want to show the image in the rstudio viewer.
The image will be visible in the html file created when you knit, if you open in a browser connected to the internet.
```{r echo=FALSE, message=FALSE, warning=FALSE}
plot(cars)
```
The problem of hovering the image duplicating the image can be fixed by removing the line below from the css file that is generated at \libs\gitbook-2.6.7\css\style.css
.book .book-header h1 a:hover{color:inherit;text-decoration:none}#media (max-width:1000px){.book .book-header h1{display:none}}
as a result, this code below places the image right above the title:
---
title: |
{width=400px style="display: block; margin:0 auto; align:center;" }
<center>GEOG380 Basic Stats with R</center>
---
I have a summary figure that I want to insert at the top of my HTML report generated using knitr/rmarkdown. But the inputs of this figure depend on outputs generated from downstream code chunks and child documents. Is there a way to do this without having to put the summary figure at the end of the document?
I have tried ref.label='last' option in the top level code chunk (with eval=FALSE) to add a duplicate code chunk in the end of the document {r last, eval=TRUE}, but has not worked for me.
Any suggestions?
You can insert HTML anywhere into your document referencing the figure by the name knitr will use for it.
To figure out the name, temporarily change the YAML header to something like this:
output:
html_document:
self_contained: FALSE
This won't embed figures in the output, they'll be kept in a separate directory. Open the output in an editor, or view source in a browser, and look for the line that displays the figure. In my test example below, it was being displayed by this code:
<p><img src="Untitled2_files/figure-html/rnormplot-1.png" width="672" /></p>
I copied that line into the document, and removed the self_contained setting, and got this source code:
---
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
This is the figure before it was generated:
<p><img src="Untitled2_files/figure-html/rnormplot-1.png" width="672" /></p>
And here it is being generated:
```{r rnormplot}
x <- rnorm(100)
plot(x)
```
One key is to name the code chunk that generates the plot (mine is named rnormplot) because that helps to make sure the figure name is independent of the rest of the document.
I try to get Highouts Output in my Powerpoint presentation, but the suggestion does not work .This feature is still pretty new and I was not able to find something valueable in the docu.
---
title: "Untitled"
output:
beamer_presentation: default
powerpoint_presentation: default
ioslides_presentation: default
always_allow_html: yes
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(highcharter)
```
### R Markdown
This is an R Markdown presentation. Markdown is a simple formatting
syntax for authoring HTML, PDF, and MS Word documents. For more
details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that
includes both content as well as the output of any embedded R code
chunks within the document.
### Slide with Bullets
- Bullet 1
- Bullet 2
- Bullet 3
### Slide with R Output
```{r cars, echo = TRUE}
highchart() %>%
hc_add_series(data = mtcars, type = "bar", hcaes(y = cyl))
```
### Slide with Plot
```{r pressure}
plot(pressure)
```
Produces:
Functions that produce HTML output found in document targeting pptx output.
Please change the output type of this document to HTML. Alternatively, you can allow
HTML output in non-HTML formats by adding this option to the YAML front-matter of
your rmarkdown file:
always_allow_html: yes
Note however that the HTML output will not be visible in non-HTML formats.
I added the always_allow_html: yes part to the top, but it still does not work. Can anyone help me?
I would like to write an R Markdown document which presents code examples of how to write an R Markdown document. For example, I want to show in the document how to render text as bold.
`**this is bold**` will render 'this is bold' with bold text, i.e. **this is bold**
That works fine, the ` render the text within as code. However, I can't figure out how to get a code chunk to display properly. e.g.
```{markdown, eval=FALSE}
```{r}
x = rnorm(1)
```
```
This doesn't work because markdown isn't a supported language. I can't enclose the r code block in ` because I need that symbol to mark the beginning of the code chunk and it only works inline.
I can do some hoop jumping by actually using R
```{r, echo="FALSE"}
o = "```{r}\nx=sample(1)\n```\n"
cat(o)
```
which renders as
## ```{r}
## x=sample(1)
## ```
But this is more complicated for me writing the document and the code it generates doesn't allow for simple copy/paste.
Is there a native way to render as code the markdown necessary to create the R code block?
I found the bookdown book on Rmarkdown which has examples of R code chunks being rendered via Rmarkdown. The book source is available on GitHub and the relevant chapter is located here.
The chunk below works as desired. I can't explain why the `r ''` is required at the beginning of the block, but it is.
````markdown
`r ''````{r}
x = sample(1)
```
````
If you don't put {r} after the three backticks, rmarkdown will just pass the block on to markdown and it almost works. For example, this
```
```{r}
x = rnorm(1)
```
```
displays as
It's not quite right; the braces around the r have been removed. (I think r-markdown did that, not markdown.) I don't know if there's an option to force them in, but they will appear if there's a non-letter ahead of the r. You can put in a space, or (if you can figure out how) a zero width space, which R will display using "\u200B".
You can use the experimental knitrhooks package, which adds the chunk option chunk_head to enable us to keep the header. The package is in development on GitHub here.
To install the package, use the command devtools::install_github("nathaneastwood/knitrhooks"). Once installed, you can use the chunk hook by loading the package and then calling the function chunk_head() in your header.
Here is an example:
---
title: "Untitled"
output: pdf_document
---
```{r, include = FALSE}
library(knitrhooks)
chunk_head()
```
```{r, chunk_head = TRUE, echo = TRUE}
x <- sample(1)
```
Unfortunately, this will not display syntax highlighting, but as discussed within this issue, this is a limitation within how knitr processes the file.