Diagnosis labels with the top 2 NMI features of each type

Number of iterations <- 10000

3 Dimensions

Perplexity = 10

tsne <- Rtsne(train[,-1], dims = 3, perplexity=10, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

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Perplexity = 20

tsne <- Rtsne(train[,-1], dims = 3, perplexity=20, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

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Perplexity = 30

tsne <- Rtsne(train[,-1], dims = 3, perplexity=30, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

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Perplexity = 40

tsne <- Rtsne(train[,-1], dims = 3, perplexity=40, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

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Perplexity = 50

tsne <- Rtsne(train[,-1], dims = 3, perplexity=50, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

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Changing up dimensions

Dimsensions = 1, Perplexity = 10

tsne <- Rtsne(train[,-1], dims = 2, perplexity=10, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])

Dimsensions = 2, Perplexity = 30

tsne <- Rtsne(train[,-1], dims = 2, perplexity=30, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])

Dimsensions = 2, Perplexity = 50

tsne <- Rtsne(train[,-1], dims = 2, perplexity=50, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])

Diagnosis labels with the top 15 NMI features

Number of iterations <- 20000

3 Dimensions

Perplexity = 10

tsne <- Rtsne(train[,-1], dims = 3, perplexity=10, verbose=FALSE, max_iter = max_iter)

plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

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Perplexity = 20

tsne <- Rtsne(train[,-1], dims = 3, perplexity=20, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

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Perplexity = 30

tsne <- Rtsne(train[,-1], dims = 3, perplexity=30, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

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Perplexity = 40

tsne <- Rtsne(train[,-1], dims = 3, perplexity=40, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

You must enable Javascript to view this page properly.

Perplexity = 50

tsne <- Rtsne(train[,-1], dims = 3, perplexity=50, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

You must enable Javascript to view this page properly.

Changing up dimensions

Dimsensions = 1, Perplexity = 10

tsne <- Rtsne(train[,-1], dims = 2, perplexity=10, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])

Dimsensions = 2, Perplexity = 30

tsne <- Rtsne(train[,-1], dims = 2, perplexity=30, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])

Dimsensions = 2, Perplexity = 50

tsne <- Rtsne(train[,-1], dims = 2, perplexity=50, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])

Diagnosis labels with all 7 clinical features

Number of iterations <- 20000

3 Dimensions

Perplexity = 10

tsne <- Rtsne(train[,-1], dims = 3, perplexity=10, verbose=FALSE, max_iter = max_iter)

plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

You must enable Javascript to view this page properly.

Perplexity = 20

tsne <- Rtsne(train[,-1], dims = 3, perplexity=20, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

You must enable Javascript to view this page properly.

Perplexity = 30

tsne <- Rtsne(train[,-1], dims = 3, perplexity=30, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

You must enable Javascript to view this page properly.

Perplexity = 40

tsne <- Rtsne(train[,-1], dims = 3, perplexity=40, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

You must enable Javascript to view this page properly.

Perplexity = 50

tsne <- Rtsne(train[,-1], dims = 3, perplexity=50, verbose=FALSE, max_iter = max_iter)
plot3d(x=tsne$Y[,1], y=tsne$Y[,2], z=tsne$Y[,3], type = 'p', col=colors[train$Labels], size=8)
legend3d("topright", legend = names(colors), pch = 16, col = colors, cex=1, inset=c(0.02))

You must enable Javascript to view this page properly.

Changing up dimensions

Dimsensions = 1, Perplexity = 10

tsne <- Rtsne(train[,-1], dims = 2, perplexity=10, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])

Dimsensions = 2, Perplexity = 30

tsne <- Rtsne(train[,-1], dims = 2, perplexity=30, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])

Dimsensions = 2, Perplexity = 50

tsne <- Rtsne(train[,-1], dims = 2, perplexity=50, verbose=FALSE, max_iter = max_iter)
plot(tsne$Y, t='n', main="tsne")
text(tsne$Y, labels=train$Labels, col=colors[train$Labels])