t-sne code and labelling issue for rna seq data

Question

I'm trying to run t-sne on my coding as well as non coding genes. Even though I'm getting output I'm not confident about my code (The output it's difficult to interpret).

I have a data set of total 16 cell type and about 3000 genes.

This is how my data is first column is gene rest is sample:

gene    H1  H2  H3  H4  M2  M3  M4  C1  C2  C3  C4  G2  G3  G4  Gran1   Gran2

The code used:

library(Rtsne)
file1<- read.csv('UNIQUE_WGCNA_FILE.csv',header = T,row.names = 1)
trn <- data.matrix(file1)
dim(trn)

tsne <- Rtsne(as.matrix(trn[,1:16]), check_duplicates = FALSE, pca = FALSE, perplexity=50, theta=0.5, dims=3)

cols <- rainbow(10)
plot(tsne$Y, t='n')
text(tsne$Y, labels=as.numeric(trn[,1]), col=cols[trn[,1]])

require(rgl)
plot3d(tsne$Y, col=cols[trn[,1]])
legend3d("topright", legend = '0':'5', pch = 16, col = rainbow(10))
rgl.postscript("Merge.pdf", "pdf")

I'm getting output but I don't know how to label so its becoming difficult. Any suggestion or help how to label would be appreciated.

Answer 1

Although a bit late, here is the solution for this:

1) Create color/column levels:

levels = unlist(lapply(colnames(trn[,1:16]), function(x)
    {

        if(x == "H1") return("H1")
        else if(x == "H2") return("H2")


}))

2)

plot(tsne$Y, col=factor(levels))

This should color columns H1 and H2 differently

Edit:

This is a sample complete code:

library(Rtsne)
file1<- read.csv('filename.csv',header = T, row.names=1)
trn <- data.matrix(file1)
dim(trn)

tsne <- Rtsne(as.matrix(trn[,1:16]), check_duplicates = FALSE, pca = FALSE, perplexity=5, theta=0.5, dims=3)

collevels = unlist(lapply(colnames(trn), function(x)
{
  if(grepl("H1",x))
    return("blue")
  else if(grepl("H2",x))
    return("red")

  # etc ... for all the columns you want to color
}
))

colorColumns = factor(collevels)
require(rgl)
plot3d(tsne$Y[,1], tsne$Y[,2], tsne$Y[,3], col=colorColumns)

Answer 2

It seems that tsne$Y is the matrix and the names are just taken from there. So, you could replace the names of the columns of that matrix and then it would display the names instead of the numbers.

But, you are using the function plot3d from the rgl package, which has as arguments xlab, ylab, and zlab, so you just need to give a string to those arguments to name the axes.