w<-E(g.toplot)$weight
tovire <- which(w<=seuil)
g.toplot <- delete.edges(g.toplot,(tovire))
- for (i in 0:(length(V(g.toplot)))) {
+ for (i in 1:(length(V(g.toplot)))) {
if (length(neighbors(g.toplot,i))==0) {
vec<-append(vec,i)
}
g.toplot <- delete.vertices(g.toplot,vec)
v.label <- V(g.toplot)$name
if (!is.logical(vec)) mat.eff <- mat.eff[-(vec)]
- }
+ } else {
+ vec <- NULL
+ }
if (!is.null(minmaxeff[1])) {
eff<-norm.vec(mat.eff,minmaxeff[1],minmaxeff[2])
we.width <- NULL
}
if (method != 'binom') {
- we.label <- round(E(g.toplot)$weight,1)
+ we.label <- round(E(g.toplot)$weight,2)
} else {
we.label <- round(E(g.toplot)$weight,3)
}
com <- NULL
}
- out <- list(graph = g.toplot, mat.eff = mat.eff, eff = eff, mat = mat.simi, v.label = v.label, we.width = we.width, we.label=we.label, label.cex = label.cex, layout = lo, communities = com, halo = halo)
+ out <- list(graph = g.toplot, mat.eff = mat.eff, eff = eff, mat = mat.simi, v.label = v.label, we.width = we.width, we.label=we.label, label.cex = label.cex, layout = lo, communities = com, halo = halo, elim=vec)
}
plot.simi <- function(graph.simi, p.type = 'tkplot',filename=NULL, communities = NULL, vertex.col = 'red', edge.col = 'black', edge.label = TRUE, vertex.label=TRUE, vertex.label.color = 'black', vertex.label.cex= NULL, vertex.size=NULL, leg=NULL, width = 800, height = 800, alpha = 0.1, cexalpha = FALSE, movie = NULL, svg = FALSE) {
}
par(pch=' ')
if (is.null(graph.simi$com)) {
- plot(g.toplot,vertex.label='', edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color='white', edge.label=we.label, edge.label.cex=cex, edge.color=edge.col, vertex.label.cex = 0, layout=lo)#, rescale = FALSE)
+ plot(g.toplot,vertex.label='', edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color='white', edge.label=we.label, edge.label.cex=cex, edge.color=edge.col, vertex.label.cex = 0, layout=lo, edge.curved=FALSE)#, rescale = FALSE)
} else {
if (graph.simi$halo) {
mark.groups <- communities(graph.simi$com)
} else {
mark.groups <- NULL
}
- plot(com, g.toplot,vertex.label='', edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color='white', edge.label=we.label, edge.label.cex=cex, edge.color=edge.col, vertex.label.cex = 0, layout=lo, mark.groups = mark.groups)
+ plot(com, g.toplot,vertex.label='', edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color='white', edge.label=we.label, edge.label.cex=cex, edge.color=edge.col, vertex.label.cex = 0, layout=lo, mark.groups = mark.groups, edge.curved=FALSE)
}
#txt.layout <- lo
txt.layout <- layout.norm(lo, -1, 1, -1, 1, -1, 1)
#rgl.open()
#par3d(cex=0.8)
lo <- layout.norm(lo, -10, 10, -10, 10, -10, 10)
+ bg3d('white')
rglplot(g.toplot,vertex.label='', edge.width=we.width/10, vertex.size=0.01, vertex.color=vertex.col, vertex.label.color="black", edge.color = edge.col, layout=lo, rescale = FALSE)
#los <- layout.norm(lo, -1, 1, -1, 1, -1, 1)
text3d(lo[,1], lo[,2], lo[,3], vire.nonascii(v.label), col = vertex.label.color, alpha = 1, cex = vertex.label.cex)