CODEWITHSUNDEEP
rr-markdownr-plotlyggplotly
fdetsch
fdetsch

Reputation: 5308

Render ggplotly() in R Markdown github_document

Interactive graphs created with ggplotly() go along nicely with html_document output in R Markdown, see eg. RMarkdown and ggplotly. For github_document output, however, the knitted HTML preview file does not show ggplotly() graphs.

I adopted the code from the linked SO post and only changed the output format in the header. Does anyone know how to render plotly graphs correctly with this kind of output? Or at least, if that is even possible?

---
title: "RmarkdownExample"
author: "fdetsch"
date: "April 16, 2020"
output: github_document
---

Here is the graph I generated. 

```{r setup, message = FALSE, echo = FALSE, warning=FALSE}
# Require
library(plotly)
# Create
dsamp <- diamonds[sample(nrow(diamonds), 1000), ]
# Plot
g <- qplot(carat, price, data=dsamp, colour=clarity)
# Call
ggplotly(g)
```

enter image description here

Upvotes: 3

Views: 1424

Answers (2)

fdetsch
fdetsch

Reputation: 5308

For output: github_document, I found a workaround that renders ggplotly() graphs nicely using iframes. The trick is to export the plotly widget as HTML and subsequently embed it as iframe. In my opinion, the advantage over output: html_document with keep_md enabled is that the online .md file simply prints a link to the intermediary HTML file instead of the full widget code, making it much tidier.

---
title: "Render `ggplotly()` graphs in `github_document`"
author: "fdetsch"
date: "`r Sys.Date()`"
output: github_document
---

Here is the graph I generated. 

```{r setup, message = FALSE, echo = FALSE, warning = FALSE}
# Require
library(plotly)
# Create
dsamp <- diamonds[sample(nrow(diamonds), 1000), ]
# Plot
g <- qplot(carat, price, data=dsamp, colour=clarity)
# Call
p <- ggplotly(g)

```

```{r include, echo = FALSE}
htmlwidgets::saveWidget(p, "index.html")

htmltools::tags$iframe(
  src=file.path(getwd(), "index.html"),
  width="100%",
  height="600",
  scrolling="no",
  seamless="seamless",
  frameBorder="0"
)

```

At least when opening the preview HTML in an external viewer, the interactive graph shows up. The RStudio (preview version 1.3.938) viewer currently fails to render the image.

Upvotes: 2

J_F
J_F

Reputation: 10352

There seem to be some problems with github_document, see here. My workaround: knit to html_document and save the resulting *.md-file. So the YAML header is:

---
title: "RmarkdownExample"
author: "fdetsch"
date: "April 16, 2020"
output: 
  html_document:
    keep_md: true
---

You can then use the md file to upload to github.

Upvotes: 1

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