do.phate {Rdimtools}

Potential of Heat Diffusion for Affinity-based Transition Embedding

Description

PHATE is a nonlinear method that is specifically targeted at visualizing high-dimensional data by embedding it on 2- or 3-dimensional space. We offer a native implementation of PHATE solely in R/C++ without interface to python module.

Usage

do.phate(
  X,
  ndim = 2,
  k = 5,
  alpha = 10,
  dtype = c("sqrt", "log"),
  smacof = TRUE,
  ...
)

Arguments

X

an (n\times p) matrix or data frame whose rows are observations and columns represent independent variables.

ndim

an integer-valued target dimension (default: 2).

k

size of nearest neighborhood (default: 5).

alpha

decay parameter for Gaussian kernel exponent (default: 10).

dtype

type of potential distance transformation; "log" or "sqrt" (default: "sqrt").

smacof

a logical; TRUE to use SMACOF for Metric MDS or FALSE to use Classical MDS (default: TRUE).

...

extra parameters including

maxiter

maximum number of iterations (default: 100).

abstol

absolute stopping criterion for metric MDS iterations (default: 1e-8).

Value

a named Rdimtools S3 object containing

Y

an (n\times ndim) matrix whose rows are embedded observations.

algorithm

name of the algorithm.

References

Moon KR, van Dijk D, Wang Z, Gigante S, Burkhardt DB, Chen WS, Yim K, van den Elzen A, Hirn MJ, Coifman RR, Ivanova NB, Wolf G, Krishnaswamy S (2019). “Visualizing Structure and Transitions in High-Dimensional Biological Data.” Nature Biotechnology, 37(12), 1482–1492. ISSN 1087-0156, 1546-1696.

Examples

## load iris data
data(iris)
X     = as.matrix(iris[,1:4])
lab   = as.factor(iris[,5])

## compare different neighborhood sizes.
pca2d <- do.pca(X, ndim=2)
phk01 <- do.phate(X, ndim=2, k=2)
phk02 <- do.phate(X, ndim=2, k=5)
phk03 <- do.phate(X, ndim=2, k=7)

## Visualize
opar <- par(no.readonly=TRUE)
par(mfrow=c(2,2))
plot(pca2d$Y, col=lab, pch=19, main="PCA")
plot(phk01$Y, col=lab, pch=19, main="PHATE:k=2")
plot(phk02$Y, col=lab, pch=19, main="PHATE:k=5")
plot(phk03$Y, col=lab, pch=19, main="PHATE:k=7")
par(opar)