phate_original: Original Version of PHATE

In kisungyou/exp3riment: some random stuffs

Description

Original Version of PHATE

Usage

phate_original(
  data,
  ndim = 2,
  nbdk = 5,
  alpha = 2,
  alg = c("cmds", "mmds"),
  potential = c("log", "sqrt", "none"),
  n_landmark = 100,
  use_landmark = TRUE
)

Arguments

data	matrix N observations
ndim	target dimension
nbdk	neighborhood size
alpha	decaying kernel parameter

Value

a list containing

transition

transition matrix of optimal kernel.

embedding

embedding matrix.

Examples

## Not run: 
# load the data
data(Embryoid, package="exp3riment")

nsample = 2000
sub_id  = sample(1:nrow(Embryoid$data), nsample)

sub_data  = Embryoid$data[sub_id,]
sub_label = Embryoid$label[sub_id]

distEB    = stats::as.dist(fast_dist(sub_data))
landmark1 = phate_original(distEB, n_landmark=100)$embedding
landmark2 = phate_original(distEB, n_landmark=250)$embedding
landmark3 = phate_original(distEB, n_landmark=500)$embedding

opar <- par(no.readonly=TRUE)
par(mfrow=c(1,3))
plot(landmark1, pch=19, col=sub_label, main="Case 1")
plot(landmark2, pch=19, col=sub_label, main="Case 2")
plot(landmark3, pch=19, col=sub_label, main="Case 3")
par(opar)

## End(Not run)

kisungyou/exp3riment documentation built on Jan. 14, 2022, 9:16 a.m.