3D Plot for Seurat

3D_plot_in_Seurat.R

counts.seurat <- RunTSNE(counts.seurat,
                         reduction.use = "pca",
                         dims.use = 1:6,
                         dim.embed = 3)

DimPlot(object = counts.seurat, reduction.use = "tsne", dim.1 = 1, dim.2 = 3)

tSNE_1 <- counts.seurat@dr$tsne@cell.embeddings[,1]
tSNE_2 <- counts.seurat@dr$tsne@cell.embeddings[,2]
tSNE_3 <- counts.seurat@dr$tsne@cell.embeddings[,3]

TSNEPlot(counts.seurat)

color_scheme <- as.numeric(1:14)[counts.seurat@ident]
for(i in 1:1521){
  if(color_scheme[i] == 1){
  color_scheme[i] <- "#F8766D"
  }else if(color_scheme[i] == 2){
  color_scheme[i] <- "#E38900"
  }else if(color_scheme[i] == 3){
  color_scheme[i] <- "#C49A00"
  }else if(color_scheme[i] == 4){
  color_scheme[i] <- "#99A800"
  }else if(color_scheme[i] == 5){
  color_scheme[i] <- "#53B400"
  }else if(color_scheme[i] == 6){
  color_scheme[i] <- "#00BC56"
  }else if(color_scheme[i] == 7){
  color_scheme[i] <- "#00C094"
  }else if(color_scheme[i] == 8){
  color_scheme[i] <- "#00BFC4"
  }else if(color_scheme[i] == 9){
  color_scheme[i] <- "#00B6EB"
  }else if(color_scheme[i] == 10){
  color_scheme[i] <- "#06A4FF"
  }else if(color_scheme[i] == 11){
  color_scheme[i] <- "#A58AFF"
  }else if(color_scheme[i] == 12){
  color_scheme[i] <- "#DF70F8"
  }else if(color_scheme[i] == 13){
  color_scheme[i] <- "#FB61D7"
  }else if(color_scheme[i] == 14){
  color_scheme[i] <- "#FF66A8"
  }else{NULL}
}

library(rgl)
plot3d(x = tSNE_1, y = tSNE_2, z = tSNE_3,
  col = color_scheme,
  type = "s", size = 0.3, box = FALSE)
rgl::rglwidget("~/Desktop/tSNE_3dplot.html") #save as html

Hi,

when i run your code it gave
Error: no slot of name "dr" for this object of class "Seurat"
I really do not know what could be

Thanks!

@joaquinhenriquez
If you are using Seurat v3 the slot name has changed.
https://satijalab.org/seurat/essential_commands.html

You can use the object[["reduction_type"]]@cell.embeddings[,n] after running your reduction with n.components = 3L

Thanks for the above code - very easy to work with!!
To ease the colouring after clusters I added a colour column to the metadata and coloured by that as follow:

colour_df <- data.frame("cluster"=as.numeric(unique(mcdc.3D@meta.data$res.0.8)[order(unique(mcdc.3D@meta.data$res.0.8))]),
                        "colour"=hue_pal()(length(unique(mcdc.3D@meta.data$res.0.8))))
colour_vec <- NULL
for (cl in as.numeric(mcdc.3D@meta.data$res.0.8)){colour_vec <- append(colour_vec,as.character(colour_df$colour[colour_df$cluster %in% cl]))}
mcdc.3D@meta.data$col0.8 <- colour_vec

plot3d(...,col=mcdc.3D@meta.data$col0.8)

My Seurat object is called mcdc.3D and I have coloured after clusters in res 0.8.
I currently use Seurat 2.4 - so adjustments might be necessary for v3.

Hi!

Is there a way to highlight a group of cells that express a gene in the 3d plot?

Best,
Joaquin

Hi Joaquin,

I haven't done it myself, but you could do it by passing the expression vector for your gene of interest through colorRampPallete. This would generate a vector of colors that you would assign to color_scheme.

Here's an example if you're using Seurat v3:

exp_vector <- seurat_obj@assays$RNA@data[grep("atoh1a",rownames(seurat_obj)),]
n_cells <- length(colnames(seurat_obj))

breaks <- cut(exp_vector, breaks = seq(min(exp_vector), max(exp_vector),
    len = n_cells), include.lowest = TRUE)

color_scheme <- colorRampPalette(c("white", "blue"))(n_cells)[breaks]

cool! I finally did it in this way,

gecko252com<- RunTSNE(combined, reduction.use = "tsne", dims.use = 1:6, dim.embed = 3)

DimPlot(object = combined, reduction.use = "tsne", dim.1 = 1, dim.2 = 3)
tSNE_1 <- combined[["tsne"]]@cell.embeddings[,1]
tSNE_2 <- combined[["tsne"]]@cell.embeddings[,2]
tSNE_3 <- combined[["tsne"]]@cell.embeddings[,3]

combined<- SetIdent(object = combined, cells = WhichCells(combined, expression = PITX2>1), value = '1')
combined <- SetIdent(object = combined, cells = WhichCells(combined, expression = PITX2<=1), value = '2')
TSNEPlot(combined)

levels(gecko252com)
Idents(gecko252com)
color_scheme <- as.numeric(1:2)[Idents(combined)]
for(i in 1:2){
if(color_scheme[i] == 1){
color_scheme[i] <- "#F8766D"
}else if(color_scheme[i] == 2){
color_scheme[i] <- "#E38900"
}else{NULL}
}

library(rgl)
open3d()
plot3d(x = tSNE_1, y = tSNE_2, z = tSNE_3,
col = color_scheme,
type = "s", size = 0.3, box = FALSE)
M <- par3d("userMatrix")
if (!rgl.useNULL())
play3d( par3dinterp(time = (0:2)*0.75, userMatrix = list(M,
rotate3d(M, pi/2, 1, 0, 0),
rotate3d(M, pi/2, 0, 1, 0) ) ),
duration = 3 )
movie3d( spin3d(), duration = 5, dir = "C:/Users/ideapad 710s plus i7/Desktop/courses")