X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=Rscripts%2Fsimi.R;h=da3aa905d8a44f08472b480a8920e6c663eec541;hp=e738a80835185fdf4b02e9e28a9f96beea4bd4e3;hb=b19770356272772c8c8ba75f351520eca186bd19;hpb=22cd27b2bbe9ab1ffa7ef06fa764b5147ae17dad diff --git a/Rscripts/simi.R b/Rscripts/simi.R index e738a80..da3aa90 100644 --- a/Rscripts/simi.R +++ b/Rscripts/simi.R @@ -114,7 +114,7 @@ BuildProf01<-function(x,classes) { 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) @@ -122,27 +122,36 @@ do.simi <- function(x, method = 'cooc',seuil = NULL, p.type = 'tkplot',layout.ty 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)$weight + } g.toplot<-g.max } if (!is.null(seuil)) { - if (seuil >= max(mat.simi)) seuil <- max(mat.simi)-1 + print(seuil) + if (seuil >= max(mat.simi)) seuil <- 0 vec<-vector() w<-E(g.toplot)$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])) { @@ -187,10 +196,32 @@ do.simi <- function(x, method = 'cooc',seuil = NULL, p.type = 'tkplot',layout.ty } 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$graph if (is.null(vertex.size)) { @@ -232,14 +263,24 @@ plot.simi <- function(graph.simi, p.type = 'tkplot',filename=NULL, vertex.col = } if (p.type=='nplot') { #print('ATTENTION - PAS OPEN FILE') - open_file_graph(filename, width = width, height = height) + open_file_graph(filename, width = width, height = height, svg = svg) par(mar=c(2,2,2,2)) if (!is.null(leg)) { layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7))) par(mar=c(2,2,1,0)) } par(pch=' ') - plot(g.toplot,vertex.label='', edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color='white', edge.label=we.label, edge.label.cex=cex, edge.color=edge.col, vertex.label.cex = 0, layout=lo) + if (is.null(graph.simi$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 { + 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) + } + #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)] @@ -268,10 +309,15 @@ plot.simi <- function(graph.simi, p.type = 'tkplot',filename=NULL, vertex.col = if (p.type == 'rgl') { library('rgl') - 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')) + #rgl.open() + #par3d(cex=0.8) + lo <- layout.norm(lo, -10, 10, -10, 10, -10, 10) + 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) + print(v.label) + 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')) if (!is.null(movie)) { require(tcltk) ReturnVal <- tkmessageBox(title="RGL 3 D",message="Cliquez pour commencer le film",icon="info",type="ok")