CanvasXpress References

A curated collection of research papers, blog posts, and tutorials that feature CanvasXpress.

How to cite CanvasXpress

If CanvasXpress contributed to your work, please cite the software paper below and the version you used.

Primary citation (software paper, 2025)

@Article{smith2025canvasxpress,
  title   = {Generating Visualizations Conversationally using Guided
             Autocomplete and LLMs},
  author  = {Smith, Andrew K. and Neuhaus, Isaac},
  journal = {Journal of Open Source Software},
  year    = {2025},
  volume  = {10},
  number  = {114},
  pages   = {7529},
  doi     = {10.21105/joss.07529},
}

R / Python packages

In R, citation("canvasXpress") prints the current entry. A BibTeX form:

@Manual{canvasXpress,
  title  = {canvasXpress: Visualization Package for CanvasXpress in R},
  author = {Isaac Neuhaus and Connie Brett},
  note   = {R package},
  url    = {https://CRAN.R-project.org/package=canvasXpress},
}

Archived version (Zenodo DOI)

Every release is archived on Zenodo with a citable DOI. The concept DOI 10.5281/zenodo.22287421 always resolves to the latest release; the Zenodo record for the exact version you used (shown on the Updates page) carries its own version DOI — cite that one for reproducibility.

Earlier method reference: canvasDesigner (Zhang, Zhao & Neuhaus, Bioinformatics 2018).

Questions & community

Ask questions, report issues, and see answers in the open at the GitHub repository: github.com/neuhausi/canvasXpress. Public, searchable threads there help the next person with the same question.

Featured Publications

Generating Visualizations Conversationally using Guided Autocomplete and LLMs. Andrew K. Smith, Isaac Neuhaus. Journal of Open Source Software, 10(114), 7529, 2025. https://doi.org/10.21105/joss.07529
In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment. Anna Lyubetskaya, Brian Rabe, Andrew Kavran, et al. (incl. Isaac Neuhaus), Eugene Drokhlyansky. Cell Reports, Vol 45, Article 116827, 2025. https://doi.org/10.1016/j.celrep.2025.116827
Assessment of spatial transcriptomics for oncology discovery. Anna Lyubetskaya, Brian Rabe, Andrew Fisher, Anne Lewin, Isaac Neuhaus, Constance Brett, Todd Brett, Ethel Pereira, Ryan Golhar, Sami Kebede, Alba Font-Tello, Kathy Mosure, Nicholas Van Wittenberghe, Konstantinos J. Mavrakis, Kenzie MacIsaac, Benjamin J. Chen, Eugene Drokhlyansky. Cell Reports Methods. Vol 2, Issue 11, November 21, 2022. https://doi.org/10.1016/j.crmeth.2022.100340
Single Cell Viewer (SCV): An interactive visualization data portal for single cell RNA sequence data. Shuoguo Wang, Constance Brett, Mohan Bolisetty, Ryan Golhar, Isaac Neuhaus, Kandasamy Ravi. https://www.biorxiv.org/content/10.1101/664789v2
canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit. Baohong, Zhang; Shanrong, Zhao; Isaac, Neuhaus. Bioinformatics, bty377. https://Doi.Org/10.1093/Bioinformatics/Bty377

Blog Posts & Tutorials

An atomic approach that injects raw data into the visualization itself to enable data and visualization to coexist within a single file. Where is the Data?
Where Did All the Bees Go? (Part 1). Lisa Cao. Aggregate Genius Inc. 2022-09-07. A Deep Dive into Bee Colony Loss with CanvasXpress and Plotly in R (Part 1)
Where Did All the Bees Go? (Part 2). Lisa Cao. Aggregate Genius Inc. 2022-09-07. A Deep Dive into Bee Colony Loss with CanvasXpress and Plotly in R (Part 2)
It Is Time to Try CanvasXpress. A Tutorial on a New Data Visualization Package for All Levels
CanvasXpress vs. Plotly: Which Data Visualization Library Is Better?. CanvasXpress vs. Plotly
cxplot: the ggplot of JavaScript. cxplot
Dashboards in 30 seconds with CanvasXpress. Dashboards
Domino Data Labs - Blog. Large Visualizations In CanvasXpress

How-To Documents

A primer using CanvasXpress with Python. HTML - Archive
A primer using CanvasXpress with ggplot in R. HTML - Archive
A primer using CanvasXpress with Reveal JS in Quarto. HTML - Archive