I have a matrix, each data point in this matrix have Binomial variable X1 to Xm, and a continuous variable Y.

I used Rtsne() in R to separate all data points by variable X1 to Xm. After that, instead of clustering them by k-mean or hcluster, what I want is to add color on all dots based on their Y values to see how the dots with different Y value are separated.

Could anyone tell me how to add color for this purpose?

The following code are used to generate the s-SNE plot and draw the plot:

tsne_model_1 = Rtsne(as.matrix(term_tsne), check_duplicates=FALSE, pca=TRUE, perplexity=10, theta=0.5, dims=2)
d_tsne_1 = as.data.frame(tsne_model_1$Y)  
ggplot(d_tsne_1, aes(x=V1, y=V2)) +  
  geom_point(size=0.25) +
  guides(colour=guide_legend(override.aes=list(size=6))) +
  xlab("") + ylab("") +
  ggtitle("t-SNE of 533 terms") +
  theme_light(base_size=20) +
  theme(axis.text.x=element_blank(),
        axis.text.y=element_blank())

term_tsne is the data matrix I used for t-SNE, colnames(term_tsne) return X1, X2....Xm, Y