#############################################################################
# EXAMPLE 1: SIA for data.read
#############################################################################
data(data.read)
dat <- data.read
res <- sia.sirt(dat , significance=.85 )
#*** plot results with igraph package
library(igraph)
plot( res$igraph.obj ) # , vertex.shape="rectangle" , vertex.size=30 )
## Not run:
# #*** plot results with qgraph package
# miceadds::library_install(qgraph)
# qgraph::qgraph( res$adj.matrix )
#
# #*** plot results with Rgraphviz package
# # Rgraphviz can only be obtained from Bioconductor
# # If it should be downloaded, select TRUE for the following lines
# if (FALSE){
# source("http://bioconductor.org/biocLite.R")
# biocLite("Rgraphviz")
# }
# # define graph
# grmatrix <- res$graph.matr
# res.graph <- new("graphNEL", nodes= res$graph.edges , edgemode="directed")
# # add edges
# RR <- nrow(grmatrix)
# for (rr in 1:RR){
# res.graph <- Rgraphviz::addEdge(grmatrix[rr,1], grmatrix[rr,2], res.graph , 1)
# }
# # define cex sizes and shapes
# V <- length(res$graph.edges)
# size2 <- rep(16,V)
# shape2 <- rep("rectangle" , V )
# names(shape2) <- names(size2) <- res$graph.edges
# # plot graph
# Rgraphviz::plot( res.graph, nodeAttrs =list("fontsize" = size2 , "shape" = shape2) )
# ## End(Not run)
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