Embedding plotly output in R markdown

Question

There is a blog entry which describes embedding from the plotly API for R into R markdown. I just used the code to create the iframe for an html document

When I have the prieview in R studio there is no error message and the iframe is created in the html document. However, it is just empty. Apparently it does not load the content somehow. I did not create the plot in the R API beforehand (but that should not matter as this is just embedding a picture into html) isn't it?

My code in r markdown as it is is currently

```{r}
library("knitr")
library("devtools")
url<-"https://plot.ly/~etpinard/251"
plotly_iframe <- paste("<iframe scrolling='no' seamless='seamless' src='", url, 
    "/800/600' width='800' height='600'></iframe>", sep = "")

```
`r I(plotly_iframe)`

Mateo Sanchez · Accepted Answer · 2015-08-22 03:42:33Z

7

We had this same issue the first time we published an RPub. Here is your code in a published RPub.

Once it's published at RPubs.com rather than in preview, the graphs should show up. You can test it by using the "open in browser" option in RPubs:

RPub

A note. I changed height to 800 and width to 650, as that graph is a bit tall. I also added a <center> tag to place it in the center of the published version.

Plotly also has a target URL for embedding. In this case, it's https://plot.ly/~etpinard/251.embed. RPubs doesn't seem to like that though. You also might play around with borderwidth to see if you can turn off the border.

That's all to say: the graphs won't show up in the preview. I believe this is a browser limitation, as RStudio doesn't allow for publishing live web content (yet).

If you're interested and would like some example code, here is the source for a blog post that has embedded Plotly and ggplot2 plots. Hope this helps! Disclosure: I work for Plotly.

Update: Aug. 21, 2015

Head to the Plotly documentation to see the R Markdown version of this answer. Printing plotly objects in the R console creates an online figure. For example:

p <- plot_ly(economics, x = date, y = uempmed, filename="r-docs/knitr-example")

If you are using knitr/R Markdown with HTML output, printing the plotly object will now embed the plot in the HTML as an iframe. If you are writing a document with R Markdown, simply printing p will embed the plot.

You can also set the width and the height of the plot with width and height code chunk parameters. For example: {r, height=800} sets the height.

If you are using Plotly Offline with R Studio, then printing the plotly object in knitr will also include the necessary plotly.js files to draw the graph: the graph is rendered locally inside the document.

To convert the knitr document to a standalone HTML file, use knitr::knit and markdown::markdownToHTML. For example:

knitr::knit('plotly-report.Rmd', 'plotly-report.md')
markdown::markdownToHTML('plotly-report.md', 'plotly-report.html')

edited Aug 22, 2015 at 3:42

answered Aug 7, 2014 at 21:38

Mateo Sanchez

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2 Comments

Frank Harrell Over a year ago

knitr documentation states the the image size specified in the chunk header is in inches regardless of whether the graphic is a plotly graph or not. Can you comment on that?

user5359531 Over a year ago

If I have a function such as make_plotly() that runs your p <- plot_ly(...) command and performs return(p), the plot appears in the RMarkdown document. However, if I call make_plotly() from within another function such as run_workflow(), then the plot no longer appears, even when I print it.

maia · Accepted Answer · 2015-02-10 04:27:06Z

2

I had to add a ".embed?width=550&height=550" after my url to make it work. See below

```{r}
library("knitr")
library("devtools")
url<-"https://plot.ly/yourplothere.embed?width=550&height=550" 
plotly_iframe <- paste("<center><iframe scrolling='no' seamless='seamless' style='border:none' src='", url, 
    "/800/1200' width='800' height='1200'></iframe><center>", sep = "")

```
`r I(plotly_iframe)`

answered Feb 10, 2015 at 4:27

maia

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