I have a large single cell dataset. Rendering all the cells at once in UMAP or a similar plot style is very, very slow.
The ABC Atlas (Brain Knowledge Platform) visualizes UMAP plots very quickly, and appears to stream data or overlay batches of cells while rendering? What visualization framework or package(s) do you use? Is this available through the Allen Institute, either as a stand-alone tool or part of a larger suite?
We have an internal tool we built to do the UMAP. But we are in the process of making it open source!
We plan on open sourcing our “visualization toolkit” by the end of the year, which is a low-level collection of JavaScript/TypeScript libraries that enable building big-data visualizations. It will contain the fundamental building blocks that we used to make the performant UMAP.
Unfortunately, that open source toolkit won’t immediately include a “plug-n-play” version of the UMAP, but that is on our roadmap.