Plotly as png in knitr/rmarkdown

Question

The following Rmarkdown renders the plotly 3D graph in HTML, but not in PDF.

Testing plotly

```{r}
library(plotly)
p <- plot_ly(data=iris, x=~Sepal.Length, y=~Sepal.Width, z=~Petal.Length, 
             color=~Species, symbols=c(0,1), type="scatter3d", mode="markers")
p
```

A snapshot of the graph appears as follows:

According to the plotly help page:

If you are using rmarkdown with HTML output, printing a plotly object in a code chunk will result in an interactive HTML graph. When using rmarkdown with non-HTML output, printing a plotly object will result in a png screenshot of the graph.

Is there a way to render the plotly graph in a PDF?

Note: The error from rmarkdown::render() is:

Error: Functions that produce HTML output found in document targeting latex 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.

Answer 1

What I do so that rendering to PDF's work but you can still have the interactive plots in other knit types and in rmarkdown files in r studio is:

this goes in the setup block (or really, anywhere early in the file):

is_pdf <- try (("pdf_document" %in% rmarkdown::all_output_formats(knitr::current_input())), silent=TRUE)
is_pdf <- (is_pdf == TRUE)

then this is used to render any plotly plot based on what kind of document you are creating:

if (is_pdf) { export(base_plot) } else {base_plot}

in the example base_plot is the name of the plot.

Answer 2

Same issue with R markdown compile error:. You need to choose what format you want to KNIT to, tried to look at mine.

---
title: "<img src='www/binary-logo.jpg' width='240'>"
subtitle: "[<span style='color:blue'>binary.com</span>](https://github.com/englianhu/binary.com-interview-question) Interview Question I"
author: "[<span style='color:blue'>®γσ, Lian Hu</span>](https://englianhu.github.io/) <img src='www/ENG.jpg' width='24'> <img src='www/RYO.jpg' width='24'>白戸則道®"
date: "`r Sys.Date()`"
output:
  tufte::tufte_html:
    toc: yes
  tufte::tufte_handout:
    citation_package: natbib
    latex_engine: xelatex
  tufte::tufte_book:
    citation_package: natbib
    latex_engine: xelatex
link-citations: yes
---

Answer 3

I have created a little workaround, which saves the plotly images locally as png-file and imports it back to the RMD file. You need the package webshot, which you can load via:

install.packages("webshot")

Further more, you need to install phantomjs via

webshot::install_phantomjs()

Then (when phantomjs is in your PATH), you can create your RMD file:

---
title: "Untitled"
output: pdf_document
---

```{r}
library(plotly)
p <- plot_ly(economics, x = ~date, y = ~unemploy / pop)

tmpFile <- tempfile(fileext = ".png")
export(p, file = tmpFile)
```
![Caption for the picture.](`r tmpFile`)

This works for me .. perhaps it's a workaround for you, too!

Answer 4

As @hrbrmstr commented, export() previously didn't support WebGL at all, but more recent versions support exporting to png via RSelenium (see help(export, package = "plotly")). If you need pdf export, you'll have to pay for a cloud account -- https://plot.ly/products/cloud/