The BIC has registered a dedicated instance of Plotly accessible at http://plotly.bic.mni.mcgill.ca. It is hosted securely on our local servers and is free to use for the entire MNI community. This message reviews the main features of BIC’s Plotly and how to start using it. (It’s a lot easier than you think!)
Plotly is for sharing and publishing graphs and data visualizations of any type. See a simple example here. 3-D renderings of complex volumes (such as MRI) can be achieved, example here. Each graph includes an interactive figure, the source data set, and scripts used to create it. Graphs in Plotly can be shared and forked in a couple simple steps.
Access to BIC’s in-house plotly is at http://plotly.bic.mni.mcgill.ca, using your McGill short user name and password, e.g. my short user name is ‘tstrau’. If you don’t know yours, I can look it up for you.
###Share directly from your code
If you use Matlab, Python or another language, sharing your graphs to Plotly can be done with one or two lines of code. For example, to send a Matlab figure to Plotly can be done with a simple command:
fig2plotly(fig, 'filename', 'matlab-bubble-chart', 'strip', false);
Follow these links for Instructions to get started with each language:
- Python - getting started
- Matlab - getting started
- R - getting started
- In each case, take note of the section ‘Special Instructions for Plotly On-Premise Users’ where the setting
plotly_domain = "http://plotly.bic.mni.mcgill.ca"is necessary so your graphs can be exported to the BIC’s dedicated Plotly.
- You can also create charts without coding by uploading CSV or Excel files at http://plotly.bic.mni.mcgill.ca/create/
Plotly CEO Jack Parmer demonstrated the tool at the Matlab BIC workshop last week. To watch his presentation, click here (30 minutes). Plotly is a Montreal-based tech startup founded in 2012 that releases most of its software under an open-source license. Several of their staff are McGill alumni.
###Plotly conference - Registration fees waived
Plotly is holding an annual user conference Plotcon on November 14-17 in New York City. CEO Jack Parmer has offered to waive all registration fees for any Neuro staff who would like to attend. Conference info here: https://plotcon.plot.ly/
###“MNI Open Research” journal uses Plotly for figures
The Tanenbaum Open Science Initiative recently announced the launch of an open access research journal MNI Open Research, a partnership with F1000. The F1000 software uses Plotly as it’s main tool for displaying interactive figures in it’s journal articles. If you plan to submit to this new journal, it is recommended to export figures into Plotly. Detailed instructions on how to do that are provided by F1000 here: https://blog.f1000.com/wp-content/uploads/2017/07/Plotly_F1000Research_instructions.pdf
###If you need help
If you would like help getting started with Plotly or have a special use case, contact the BIC data team at firstname.lastname@example.org, or post a reply below.
The BIC will continue to support cutting-edge software for data hosting and sharing, in close cooperation with the Neuro’s Open Science Initiative.