mat
}
-do.simi <- function(x, method = 'cooc',seuil = NULL, p.type = 'tkplot',layout.type = 'frutch', max.tree = TRUE, coeff.vertex=NULL, coeff.edge = NULL, minmaxeff=c(NULL,NULL), vcexminmax= c(NULL,NULL), cex = 1, coords = NULL) {
+do.simi <- function(x, method = 'cooc',seuil = NULL, p.type = 'tkplot',layout.type = 'frutch', max.tree = TRUE, coeff.vertex=NULL, coeff.edge = NULL, minmaxeff=c(NULL,NULL), vcexminmax= c(NULL,NULL), cex = 1, coords = NULL, communities = NULL, halo = FALSE) {
mat.simi <- x$mat
mat.eff <- x$eff
v.label <- colnames(mat.simi)
g.toplot<-g1
weori<-get.edge.attribute(g1,'weight')
if (max.tree) {
- invw<-1/weori
+ if (method == 'cooc') {
+ invw<-1/weori
+ } else {
+
+ }
E(g1)$weight<-invw
g.max<-minimum.spanning.tree(g1)
E(g.max)$weight<-1/E(g.max)$weight
}
if (!is.null(seuil)) {
- if (seuil >= max(mat.simi)) seuil <- max(mat.simi)-1
+ print(seuil)
+ if (seuil >= max(mat.simi)) seuil <- 0
vec<-vector()
w<-E(g.toplot)$weight
tovire <- which(w<=seuil)
- g.toplot <- delete.edges(g.toplot,(tovire-1))
- for (i in 0:(length(V(g.toplot))-1)) {
+ g.toplot <- delete.edges(g.toplot,(tovire))
+ for (i in 0:(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)$name
- if (!is.logical(vec)) mat.eff <- mat.eff[-(vec+1)]
+ if (!is.logical(vec)) mat.eff <- mat.eff[-(vec)]
}
if (!is.null(minmaxeff[1])) {
} else {
lo <- coords
}
- out <- list(graph = g.toplot, mat.eff = mat.eff, eff = eff, mat = mat.simi, v.label = v.label, we.width = we.width, we.label=we.label, label.cex = label.cex, layout = lo)
+ if (!is.null(communities)) {
+ if (communities == 0 ){ #'edge.betweenness.community') {
+ com <- edge.betweenness.community(g.toplot)
+ } else if (communities == 1) {
+ com <- fastgreedy.community(g.toplot)
+ } else if (communities == 2) {
+ com <- label.propagation.community(g.toplot)
+ } else if (communities == 3) {
+ com <- leading.eigenvector.community(g.toplot)
+ } else if (communities == 4) {
+ com <- multilevel.community(g.toplot)
+ } else if (communities == 5) {
+ com <- optimal.community(g.toplot)
+ } else if (communities == 6) {
+ com <- spinglass.community(g.toplot)
+ } else if (communities == 7) {
+ com <- walktrap.community(g.toplot)
+ }
+ } else {
+ com <- NULL
+ }
+
+ out <- list(graph = g.toplot, mat.eff = mat.eff, eff = eff, mat = mat.simi, v.label = v.label, we.width = we.width, we.label=we.label, label.cex = label.cex, layout = lo, communities = com, halo = halo)
}
-plot.simi <- function(graph.simi, p.type = 'tkplot',filename=NULL, vertex.col = 'red', edge.col = 'black', edge.label = TRUE, vertex.label=TRUE, vertex.label.color = 'black', vertex.label.cex= NULL, vertex.size=NULL, leg=NULL, width = 800, height = 800, alpha = 0.1, cexalpha = FALSE, movie = NULL) {
+plot.simi <- function(graph.simi, p.type = 'tkplot',filename=NULL, communities = NULL, vertex.col = 'red', edge.col = 'black', edge.label = TRUE, vertex.label=TRUE, vertex.label.color = 'black', vertex.label.cex= NULL, vertex.size=NULL, leg=NULL, width = 800, height = 800, alpha = 0.1, cexalpha = FALSE, movie = NULL, svg = FALSE) {
mat.simi <- graph.simi$mat
g.toplot <- graph.simi$graph
if (is.null(vertex.size)) {
}
if (p.type=='nplot') {
#print('ATTENTION - PAS OPEN FILE')
- open_file_graph(filename, width = width, height = height)
+ open_file_graph(filename, width = width, height = height, svg = svg)
par(mar=c(2,2,2,2))
if (!is.null(leg)) {
layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7)))
par(mar=c(2,2,1,0))
}
par(pch=' ')
- plot(g.toplot,vertex.label='', edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color='white', edge.label=we.label, edge.label.cex=cex, edge.color=edge.col, vertex.label.cex = 0, layout=lo)
+ if (is.null(graph.simi$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)
+ } else {
+ com <- graph.simi$com
+ colm <- rainbow(length(com))
+ if (vertex.size != 0 || graph.simi$halo) {
+ vertex.label.color <- 'black'
+ vertex.col <- colm[membership(com)]
+ } else {
+ vertex.label.color <- colm[membership(com)]
+ }
+ if (graph.simi$halo) {
+ mark.groups <- communities(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)
+ }
+ #txt.layout <- lo
txt.layout <- layout.norm(lo, -1, 1, -1, 1, -1, 1)
#txt.layout <- txt.layout[order(label.cex),]
#vertex.label.color <- vertex.label.color[order(label.cex)]
if (p.type == 'rgl') {
library('rgl')
+ #rgl.open()
+ #par3d(cex=0.8)
rglplot(g.toplot,vertex.label= vire.nonascii(v.label), edge.width=we.width/10, vertex.size=0.01, vertex.color=vertex.col, vertex.label.color="black", edge.color = edge.col, layout=lo)
los <- layout.norm(lo, -1, 1, -1, 1, -1, 1)
rgl.spheres(los, col = vertex.col, radius = vertex.size/100, alpha = alpha)
nm[,index] <- mat.simi[,index]
nm[index,] <- mat.simi[index,]
nm
+# cs <- colSums(nm)
+# if (cs) nm <- nm[,-which(cs==0)]
+# rs <- rowSums(nm)
+# if (rs) nm <- nm[-which(rs==0),]
+# nm
}