Question: Making a 3d tSNE Plot in Seurat for scRNA-seq
0
gravatar for asyndeton17
21 months ago by
asyndeton1720
asyndeton1720 wrote:

Hi,

Is there an easy way to make a 3D tSNE plot of the single cell clusters in Seurat?

Thanks

seurat rna-seq tsne scrna-seq • 4.5k views
ADD COMMENTlink modified 22 days ago by DrAcula0 • written 21 months ago by asyndeton1720

Is there a way to do so with another package?

ADD REPLYlink written 21 months ago by asyndeton1720
2
gravatar for garyhokawai
19 months ago by
garyhokawai30
garyhokawai30 wrote:

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

ADD COMMENTlink modified 19 months ago by WouterDeCoster39k • written 19 months ago by garyhokawai30

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 19 months ago by WouterDeCoster39k
0
gravatar for halo22
21 months ago by
halo22120
Indianapolis, IN
halo22120 wrote:

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.

ADD COMMENTlink written 21 months ago by halo22120
1

A bit late by now, but I think the R package Rtsne is preferable over tsne since it is faster being a wrapper over C++ code.

ADD REPLYlink written 19 months ago by dariober10k
0
gravatar for DrAcula
22 days ago by
DrAcula0
University of Miami
DrAcula0 wrote:

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

ADD COMMENTlink modified 22 days ago • written 22 days ago by DrAcula0
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