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fig1_tSNE.R
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load("IDCSCmatrix.Rda")
load("IDCSCmeta.Rda")
rownames(matrix3)<-matrix3$circRNA
matrix3$circRNA<-NULL
quantile(rowSums(as.matrix(matrix3[1:584])> 0),0.6)
quantile(rowSums(as.matrix(matrix3[1:584])> 0),0.7)
quantile(rowSums(as.matrix(matrix3[1:584])> 0),0.8)
quantile(rowSums(as.matrix(matrix3[1:584])> 0),0.9)
matrix3q<-matrix3[which(rowSums(as.matrix(matrix3)> 0)>=1&rowSums(as.matrix(matrix3)> 0)<2),]
matrix3q6<-matrix3[which(rowSums(as.matrix(matrix3)> 0)>=2&rowSums(as.matrix(matrix3)> 0)<4),]
matrix3q7<-matrix3[which(rowSums(as.matrix(matrix3)> 0)>=4&rowSums(as.matrix(matrix3)> 0)<7),]
matrix3q8<-matrix3[which(rowSums(as.matrix(matrix3)> 0)>=7&rowSums(as.matrix(matrix3)> 0)<20),]
matrix3q9<-matrix3[which(rowSums(as.matrix(matrix3)> 0)>=20),]
dat<-matrix3q9 #according to which range is to be analyzed
###############################################################
###t-SNE
library(Rtsne)
tsne<-as.data.frame(t(dat))
tsne<-unique(tsne)
set.seed(42)
sne_out1 <- Rtsne(as.matrix(tsne), dims=3, pca =T, perplexity = 50, max_iter = 500)
sne_out2 <- Rtsne(as.matrix(tsne), dims=3, pca =T, perplexity = 100, max_iter = 500)
sne_out3 <- Rtsne(as.matrix(tsne), dims=3, pca =T, perplexity = 5, max_iter = 500)
sne_out4 <- Rtsne(as.matrix(tsne), dims=3, pca =T, perplexity = 10, max_iter = 500)
sne_out5 <- Rtsne(as.matrix(tsne), dims=3, pca =T, perplexity = 25 , max_iter = 500)
samples<-as.data.frame(rownames(tsne))
colnames(samples)<-"Samples"
meta5<-merge(samples,meta4,all=F)
color1<-gsub("cancer","tomato",meta5$Type)
color1<-gsub("normal","dodgerblue",color1)
color2<-rainbow(length(meta5$Site))
library(scatterplot3d)
pdf("tsne50cannor.pdf")
scatterplot3d(sne_out1$Y,color=color1,pch=16)
dev.off()
pdf("tsne50site.pdf")
scatterplot3d(sne_out1$Y,color=color2,pch=16)
dev.off()
pdf("tsne100cannor.pdf")
scatterplot3d(sne_out2$Y,color=color1,pch=16)
dev.off()
pdf("tsne100site.pdf")
scatterplot3d(sne_out2$Y,color=color2,pch=16)
dev.off()
pdf("tsne5cannor.pdf")
scatterplot3d(sne_out3$Y,color=color1,pch=16)
dev.off()
pdf("tsne5site.pdf")
scatterplot3d(sne_out3$Y,color=color2,pch=16)
dev.off()
pdf("tsne10cannor.pdf")
scatterplot3d(sne_out4$Y,color=color1,pch=16)
dev.off()
pdf("tsne10site.pdf")
scatterplot3d(sne_out4$Y,color=color2,pch=16)
dev.off()
pdf("tsne25cannor.pdf")
scatterplot3d(sne_out5$Y,color=color1,pch=16)
dev.off()
pdf("tsne25site.pdf")
scatterplot3d(sne_out5$Y,color=color2,pch=16)
dev.off()