Plotly graphs in jupyter notebooks re-render entire page html
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- Dominant language
- R
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Description
When attempting to run the first graph in the getting started documents, after following the steps here, the entire page html is output ontop of the graph like in the screenshot below. This occurs for all other graphs I've tried as well.
library(plotly)
fig <- plot_ly(midwest, x = ~percollege, color = ~state, type = "box")
fig

Steps to Reproduce:
- pull the
jupyter/r-notebookdocker image from here with the commanddocker pull jupyter/r-notebook
a. This allows you to skip the "add r-kernel" steps because the R kernel is included with the r-notebook. Specifically these two lines can be skipped:
devtools::install_github('IRkernel/IRkernel')
IRkernel::installspec()
Alternatively, start with the jupyter/minimal-notebook and do the steps to add the R kernel.
- Run the docker image with
docker run -p '8888:8888' -e JUPYTER_ENABLE_LAB=yes jupyter/r-notebook - Open an R console and run
install.packages(c('repr', 'IRdisplay', 'pbdZMQ', 'devtools'))from the setup steps - Install pandoc - get to the container bash as root user. First get the container ID with
docker psthen use the ID you see there indocker exec -u root -ti <container id> bash. Runapt updatethenapt install pandoc.
a. Open the notebook from the link that step 2 output and you can verify pandoc is installed in/usr/bin/pandocby opening a terminal and navigating to the/usr/bindirectory. - Install plotly - either use the R console or the terminal. Personally, I used the terminal and ran
conda install r-plotly. I attempted with both the latest version and also withv4.9.2.2. Both showed the issue. - Once that's all setup, open an R-kernel notebook and attempt to create any plotly graph. It will initially load the graph correctly, then a few seconds later, you will see the issue from the screenshot above.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the linked R-in-Jupyter getting-started instructions and reproduce the example in a jupyter/r-notebook Docker container using an R-kernel notebook. Compare the initial graph rendering with the later output described in the issue; done means Plotly graphs render without appending the entire page HTML over the graph.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, jupyter-notebook, r
- Domain
- data-visualization
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100