## two dimensional Isomap embedding of a 1.000 dimensional dataset using k=5 neighbours
d = generateData(samples=20, genes=1000, diffgenes=100, blocksize=10)
d_low = Isomap(data=d[[1]], dims=2, k=5)
## Isomap residuals for target dimensions 1-10
d_low = Isomap(data=d[[1]], dims=1:10, k=5, plotResiduals=TRUE)
## three dimensional Isomap embedding of a 1.000 dimensional dataset using k=10 (nearest and farthest) neighbours
d = generateData(samples=20, genes=1000, diffgenes=100, blocksize=10)
d_low = Isomap(data=d[[1]], dims=3, mod=TRUE, k=10)
Run the code above in your browser using DataLab