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