Use seriation package to find good orderings
seriation.find.orderings(dl, .methods = c("TSP", "R2E", "HC", "GW",
"OLO"), scaled = c("scaled", "unscaled"), dim.red = c("none", "pca",
"kfa", "ica", "mds"), dims = geom.series(base = 2, max = min(8,
nrow(dl$expr) - 1)), num.cores = default.num.cores(),
num.tau.to.keep = default.num.cores())
de.lorean object
The seriation methods to apply
Whether to use the scaled and/or unscaled expression data
Dimension reduction methods to apply
Number of dimensions to reduce to
Number of cores to use in parallel
How many initialisations to keep