matrix2graph {SOMMD} | R Documentation |
Convert transition matrix to an igraph object
Description
Function to convert a transition matrix to an igraph object
Usage
matrix2graph(trans, SOM, SOM.hc, col.set, diag = FALSE)
Arguments
trans |
a transition matrix (usually obtained from comp.trans.mat) |
SOM |
a kohonen object that form the network |
SOM.hc |
a vector of cluster assignment for SOM neurons |
col.set |
a vector of colors used for the SOM clusters |
diag |
boolean condition to include diagonal elements |
Value
An igraph object, with SOM properties annotated
Author(s)
Stefano Motta stefano.motta@unimib.it
Examples
#Read example SOM data
som_model <- readRDS(system.file("extdata", "SOM_HIFa.rds", package = "SOMMD"))
#Divide the SOM in the selected number of clusters
som_cl <- cutree(hclust(dist(som_model$codes[[1]], method="euclidean"), method="complete"), 4)
#Compute transition matrix
tr_mat <- comp.trans.mat(som_model, start = 1)
#Define a set of colors
colors <- c("#1f78b4", "#33a02c", "#e31a1c", "#ffff88", "#6a3d9a")
#Create graph object
net <- matrix2graph(tr_mat, som_model, som_cl, colors, diag=FALSE)
[Package SOMMD version 0.1.2 Index]