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 {
+ invw <- 1 - weori
+ }
E(g1)$weight<-invw
g.max<-minimum.spanning.tree(g1)
- E(g.max)$weight<-1/E(g.max)$weight
+ if (method == 'cooc') {
+ E(g.max)$weight<-1 / E(g.max)$weight
+ } else {
+ E(g.max)$weight<-1 - E(g.max)$weight
+ }
g.toplot<-g.max
}
if (!is.null(seuil)) {
- if (seuil >= max(mat.simi)) seuil <- max(mat.simi)-1
+ if (seuil >= max(mat.simi)) seuil <- 0
vec<-vector()
w<-E(g.toplot)$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 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)$name
- if (!is.logical(vec)) mat.eff <- mat.eff[-(vec+1)]
- }
+ if (!is.logical(vec)) mat.eff <- mat.eff[-(vec)]
+ } else {
+ vec <- NULL
+ }
if (!is.null(minmaxeff[1])) {
eff<-norm.vec(mat.eff,minmaxeff[1],minmaxeff[2])
we.width <- NULL
}
if (method != 'binom') {
- we.label <- round(E(g.toplot)$weight,1)
+ we.label <- round(E(g.toplot)$weight,2)
} else {
we.label <- round(E(g.toplot)$weight,3)
}
- if (p.type=='rgl') {
+ if (p.type=='rgl' || p.type=='rglweb') {
nd<-3
} else {
nd<-2
} 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, elim=vec)
}
-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, edge.curved = TRUE, 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)#, rescale = FALSE)
+ if (is.null(graph.simi$com)) {
+ plot(g.toplot,vertex.label='', edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color='white', edge.label=we.label, edge.label.cex=cex, edge.color=edge.col, vertex.label.cex = 0, layout=lo, edge.curved=edge.curved)#, rescale = FALSE)
+ } else {
+ if (graph.simi$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, edge.curved=edge.curved)
+ }
#txt.layout <- lo
txt.layout <- layout.norm(lo, -1, 1, -1, 1, -1, 1)
#txt.layout <- txt.layout[order(label.cex),]
return(coords)
}
- if (p.type == 'rgl') {
+ if (p.type == 'rgl' || p.type == 'rglweb') {
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)
- rgl.bg(color = c('white','black'))
+ 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)
+ rgl.spheres(lo, col = vertex.col, radius = vertex.size/100, alpha = alpha)
+ #rgl.bg(color = c('white','black'))
+ #bg3d('white')
if (!is.null(movie)) {
require(tcltk)
ReturnVal <- tkmessageBox(title="RGL 3 D",message="Cliquez pour commencer le film",icon="info",type="ok")
ReturnVal <- tkmessageBox(title="RGL 3 D",message="Film fini !",icon="info",type="ok")
}
#play3d(spin3d(axis=c(0,1,0),rpm=6))
- require(tcltk)
- ReturnVal <- tkmessageBox(title="RGL 3 D",message="Cliquez pour fermer",icon="info",type="ok")
+ if (p.type == 'rglweb') {
+ writeWebGL(dir = filename, width = width, height= height)
+ } else {
+ require(tcltk)
+ ReturnVal <- tkmessageBox(title="RGL 3 D",message="Cliquez pour fermer",icon="info",type="ok")
+ }
rgl.close()
# while (rgl.cur() != 0)
# Sys.sleep(0.5)
+ } else if (p.type == 'web') {
+ library(rgexf)
+ simi.to.gexf(filename, graph.simi, nodes.attr = NULL)
}
}
nm[index,] <- mat.simi[index,]
nm
}
+
+#from :
+#http://gopalakrishna.palem.in/iGraphExport.html#GexfExport
+# Converts the given igraph object to GEXF format and saves it at the given filepath location
+# g: input igraph object to be converted to gexf format
+# filepath: file location where the output gexf file should be saved
+#
+saveAsGEXF = function(g, filepath="converted_graph.gexf")
+{
+ require(igraph)
+ require(rgexf)
+
+ # gexf nodes require two column data frame (id, label)
+ # check if the input vertices has label already present
+ # if not, just have the ids themselves as the label
+ if(is.null(V(g)$label))
+ V(g)$label <- as.character(V(g))
+
+ # similarily if edges does not have weight, add default 1 weight
+ if(is.null(E(g)$weight))
+ E(g)$weight <- rep.int(1, ecount(g))
+
+ nodes <- data.frame(cbind(1:vcount(g), V(g)$label))
+ nodes[,1] <- as.character(nodes[,1])
+ nodes[,2] <- as.character(nodes[,2])
+ edges <- t(Vectorize(get.edge, vectorize.args='id')(g, 1:ecount(g)))
+
+ # combine all node attributes into a matrix (and take care of & for xml)
+ vAttrNames <- setdiff(list.vertex.attributes(g), "label")
+ for (val in c("x","y","color")) {
+ vAttrNames <- setdiff(vAttrNames, val)
+ }
+ nodesAtt <- data.frame(sapply(vAttrNames, function(attr) sub("&", "&",get.vertex.attribute(g, attr))))
+ for (i in 1:ncol(nodesAtt)) {
+ nodesAtt[,i] <- as.character(nodesAtt[,i])
+ }
+
+ # combine all edge attributes into a matrix (and take care of & for xml)
+ eAttrNames <- setdiff(list.edge.attributes(g), "weight")
+ edgesAtt <- data.frame(sapply(eAttrNames, function(attr) sub("&", "&",get.edge.attribute(g, attr))))
+
+ # combine all graph attributes into a meta-data
+ graphAtt <- sapply(list.graph.attributes(g), function(attr) sub("&", "&",get.graph.attribute(g, attr)))
+ ll <- length(V(g)$x)
+ cc <- t(sapply(V(g)$color, col2rgb, alpha=TRUE))
+ cc[,4] <- cc[,4]/255
+ # generate the gexf object
+ output <- write.gexf(nodes, edges,
+ edgesWeight=E(g)$weight,
+ edgesAtt = edgesAtt,
+ #edgesVizAtt = list(size=as.matrix(E(g)$weight)),
+ nodesAtt = nodesAtt,
+ nodesVizAtt=list(color=cc, position=cbind(V(g)$x,V(g)$y, rep(0,ll)), size=V(g)$weight),
+ meta=c(list(creator="iramuteq", description="igraph -> gexf converted file", keywords="igraph, gexf, R, rgexf"), graphAtt))
+
+ print(output, filepath, replace=T)
+}
projects / iramuteq / blobdiff