I tried solution from halo22, it didn't work. However, I somehow figured it out myself.

#3d tsne projection
yourseuratobject <- RunTSNE(object = yourseuratobject, dims.use = 1:n, do.fast = TRUE, dim.embed = 3)

tsne_1 <- yourseuratobject@dr$tsne@cell.embeddings[,1]

tsne_2 <- yourseuratobject@dr$tsne@cell.embeddings[,2]

tsne_3 <- yourseuratobject@dr$tsne@cell.embeddings[,3]

library(scatterplot3d)

scatterplot3d(x = tsne_1, y = tsne_2, z = tsne_3, color = as.numeric(1:n)[yourseuratobject@ident])

library(rgl) #interactive 3d plotting

plot3d(x = tsne_1, y = tsne_2, z = tsne_3, col = as.numeric(1:n)[yourseuratobject@ident], type="s",radius=0.3)

rgl::rglwidget() #save as html

PS: tsne coordinates are stored in yourseuratobject@dr$tsne@cell.embeddings cluster identity by SNN is store in yourseuratobject@ident

ref. https://github.com/jkrijthe/Rtsne/issues/12

Hope this would help!

Gary

You can use the R-package tsne to do this https://cran.r-project.org/web/packages/tsne/tsne.pdf

For your analysis you will have to figure out what input to provide to tSNE, ideally PC's obtained from seurat are the suggested input but you can also use your variable genes with scaled values.

I know this is old now. But Ive written some code which will help you create a 3D expression plot using plotly out of a seurat v3.0.0 object. Dont forget to star and fork :)

Find the complete solution here: https://github.com/Dragonmasterx87/3D-Plotting-in-Seurat-3.0.0

Update: The code now supports UMAP 3D clustering as well :)