phate_graph: Graphical PHATE for using Effective Resistance

In kisungyou/exp3riment: some random stuffs

Description

Graphical PHATE for using Effective Resistance

Usage

phate_graph(
  input,
  ndim = 2,
  nbdk = 5,
  alpha = 2,
  alg = c("cmds", "mmds"),
  potential = c("log", "sqrt", "none"),
  n_landmark = 100
)

Examples

## Not run: 
# load the data
data("dolphins", package="exp3riment")
dat_graph = dolphins$igraph
dat_label = dolphins$label

# try PHATE
dol_log_cmds = phate_graph(dat_graph, potential="log", alg="cmds", n_landmark=50)
dol_log_mmds = phate_graph(dat_graph, potential="log", alg="mmds", n_landmark=50)

# visualize
require("igraph")
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,3))
plot(dat_graph, vertex.color=dat_label, vertex.label=NA,
     main="igraph")
plot(dat_graph, vertex.color=dat_label, vertex.label=NA,
     main="PHATE+CMDS", layout=dol_log_cmds$embedding)
plot(dat_graph, vertex.color=dat_label, vertex.label=NA,
     main="PHATE+MMDS", layout=dol_log_mmds$embedding)
par(opar)

## End(Not run)

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