gePHATE: Graph Embedding with PHATE

In kisungyou/T4network: Tools for Network Analysis

Description

Graph Embedding with PHATE

Usage

gePHATE(graph, ndim = 2, nnbd = 5, alpha = 2, ...)

Examples

## load the karate club data
data(karate, package="T4network")

## extract the label
karate.lab = karate$label

## gePHATE with different metrizations
karate.eff = gePHATE(karate$A, metrize="effective")

## prepare for igraph plotting tools
obj.igraph = igraph::graph_from_adjacency_matrix(karate$A, mode="undirected")

## visualize
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,2))
plot(obj.igraph, vertex.color=karate.lab, vertex.label=NA,
     main="igraph visualization")
plot(obj.igraph, vertex.color=karate.lab, vertex.label=NA, 
     layout=karate.eff$embed, main="gePHATE-effective")
par(opar)

kisungyou/T4network documentation built on Dec. 21, 2021, 6:44 a.m.