#from proxy package ############################################################# #a, b, c, and d are the counts of all (TRUE, TRUE), (TRUE, FALSE), (FALSE, TRUE), and (FALSE, FALSE) # n <- a + b + c + d = nrow(x) make.a <- function(x) { a <- t(x) %*% (x) a } make.b <- function(x) { b <- t(x) %*% (1 - x) b } make.c <- function(x) { c <- (1-t(x)) %*% x c } make.d <- function(x, a, b, c) { #??????????? ncol ? d <- ncol(x) - a - b - c d } ########################################### #x, a ########################################### my.jaccard <- function(x) { a <- make.a(x) b <- make.b(x) c <- make.c(x) d <- make.d(x, a, b, c) jac <- a / (a + b + c) jac } prcooc <- function(x, a) { prc <- (a / nrow(x)) prc } make.bin <- function(cs, a, i, j, nb) { if (a[i, j] >= 1) { ab <- a[i, j] - 1 res <- binom.test(ab, nb, (cs[i]/nb) * (cs[j]/nb), "less") } else { res <- NULL res$p.value <- 0 } #res <- binom.test(ab, nb, (cs[i]/nb) * (cs[j]/nb), "less") res$p.value } binom.sim <- function(x) { a <- make.a(x) n <- nrow(x) cs <- colSums(x) mat <- matrix(0,ncol(x),ncol(x)) colnames(mat)<-colnames(a) rownames(mat)<-rownames(a) for (i in 1:(ncol(x)-1)) { for (j in (i+1):ncol(x)) { mat[j,i] <- make.bin(cs, a, i, j , n) } } # print(mat) mat } ############################################ # a, b, c ############################################ # jaccard a, b, c a / (a + b + c) # Kulczynski1 a, b, c a / (b + c) # Kulczynski2 a, b, c [a / (a + b) + a / (a + c)] / 2 # Mountford a, b, c 2a / (ab + ac + 2bc) # Fager, McGowan a, b, c a / sqrt((a + b)(a + c)) - 1 / 2 sqrt(a + c) # Russel, Rao a (a/n) # Dice, Czekanowski, Sorensen a, b, c 2a / (2a + b + c) # Mozley, Margalef a, b, c an / (a + b)(a + c) # Ochiai a, b, c a / sqrt[(a + b)(a + c)] # Simpson a, b, c a / min{(a + b), (a + c)} # Braun-Blanquet a, b, c a / max{(a + b), (a + c)} #simple matching, Sokal/Michener a, b, c, d, ((a + d) /n) # Hamman, a, b, c, d, ([a + d] - [b + c]) / n # Faith , a, b, c, d, (a + d/2) / n # Tanimoto, Rogers a, b, c, d, (a + d) / (a + 2b + 2c + d) # Phi a, b, c, d (ad - bc) / sqrt[(a + b)(c + d)(a + c)(b + d)] # Stiles a, b, c, d log(n(|ad-bc| - 0.5n)^2 / [(a + b)(c + d)(a + c)(b + d)]) # Michael a, b, c, d 4(ad - bc) / [(a + d)^2 + (b + c)^2] # Yule a, b, c, d (ad - bc) / (ad + bc) # Yule2 a, b, c, d (sqrt(ad) - sqrt(bc)) / (sqrt(ad) + sqrt(bc)) BuildProf01<-function(x,classes) { #x : donnees en 0/1 #classes : classes de chaque lignes de x dm<-cbind(x,cl=classes) clnb=length(summary(as.data.frame(as.character(classes)),max=100)) print(clnb) print(summary(as.data.frame(as.character(classes)),max=100)) mat<-matrix(0,ncol(x),clnb) rownames(mat)<-colnames(x) for (i in 1:clnb) { dtmp<-dm[which(dm$cl==i),] for (j in 1:(ncol(dtmp)-1)) { mat[j,i]<-sum(dtmp[,j]) } } mat } do.simi <- function(x, method = 'cooc',seuil = NULL, p.type = 'tkplot',layout.type = 'frutch', max.tree = TRUE, coeff.vertex=NULL, coeff.edge = NULL, minmaxeff=c(NULL,NULL), vcexminmax= c(NULL,NULL), cex = 1, coords = NULL, communities = NULL, halo = FALSE) { mat.simi <- x$mat mat.eff <- x$eff v.label <- colnames(mat.simi) g1<-graph.adjacency(mat.simi,mode="lower",weighted=TRUE) g.toplot<-g1 weori<-get.edge.attribute(g1,'weight') if (max.tree) { if (method == 'cooc') { invw <- 1 / weori } else { invw <- 1 - weori } E(g1)$weight<-invw g.max<-minimum.spanning.tree(g1) 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 <- 0 vec<-vector() w<-E(g.toplot)$weight tovire <- which(w<=seuil) g.toplot <- delete.edges(g.toplot,(tovire)) for (i in 1:(length(V(g.toplot)))) { if (length(neighbors(g.toplot,i))==0) { vec<-append(vec,i) } } g.toplot <- delete.vertices(g.toplot,vec) v.label <- V(g.toplot)$name if (!is.logical(vec)) mat.eff <- mat.eff[-(vec)] } else { vec <- NULL } if (!is.null(minmaxeff[1])) { eff<-norm.vec(mat.eff,minmaxeff[1],minmaxeff[2]) } else { eff<-coeff.vertex } if (!is.null(vcexminmax[1])) { label.cex = norm.vec(mat.eff, vcexminmax[1], vcexminmax[2]) } else { label.cex = cex } if (!is.null(coeff.edge)) { we.width <- norm.vec(abs(E(g.toplot)$weight), coeff.edge[1], coeff.edge[2]) #we.width <- abs((E(g.toplot)$weight/max(abs(E(g.toplot)$weight)))*coeff.edge) } else { we.width <- NULL } if (method != 'binom') { we.label <- round(E(g.toplot)$weight,2) } else { we.label <- round(E(g.toplot)$weight,3) } if (p.type=='rgl' || p.type=='rglweb') { nd<-3 } else { nd<-2 } if (is.null(coords)) { if (layout.type == 'frutch') lo <- layout.fruchterman.reingold(g.toplot,dim=nd)#, weightsA=E(g.toplot)$weight) if (layout.type == 'kawa') lo <- layout.kamada.kawai(g.toplot,dim=nd) if (layout.type == 'random') lo <- layout.random(g.toplot,dim=nd) if (layout.type == 'circle' & p.type != 'rgl') lo <- layout.circle(g.toplot) if (layout.type == 'circle' & p.type == 'rgl') lo <- layout.sphere(g.toplot) if (layout.type == 'graphopt') lo <- layout.graphopt(g.toplot) } else { lo <- coords } 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, 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, bg='white') { mat.simi <- graph.simi$mat g.toplot <- graph.simi$graph if (is.null(vertex.size)) { vertex.size <- graph.simi$eff } else { vertex.size <- vertex.size } we.width <- graph.simi$we.width if (vertex.label) { #v.label <- vire.nonascii(graph.simi$v.label) v.label <- graph.simi$v.label } else { v.label <- NA } if (edge.label) { we.label <- graph.simi$we.label } else { we.label <- NA } lo <- graph.simi$layout if (!is.null(vertex.label.cex)) { label.cex<-vertex.label.cex } else { label.cex = graph.simi$label.cex } if (cexalpha) { alphas <- norm.vec(label.cex, 0.5,1) nvlc <- NULL if (length(vertex.label.color) == 1) { for (i in 1:length(alphas)) { nvlc <- append(nvlc, adjustcolor(vertex.label.color, alpha=alphas[i])) } } else { for (i in 1:length(alphas)) { nvlc <- append(nvlc, adjustcolor(vertex.label.color[i], alpha=alphas[i])) } } vertex.label.color <- nvlc } if (p.type=='nplot') { #print('ATTENTION - PAS OPEN FILE') open_file_graph(filename, width = width, height = height, svg = svg) par(mar=c(2,2,2,2)) par(bg=bg) if (!is.null(leg)) { layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7))) par(mar=c(2,2,1,0)) } par(pch=' ') if (is.null(graph.simi$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),] #vertex.label.color <- vertex.label.color[order(label.cex)] #v.label <- v.label[order(label.cex)] #label.cex <- label.cex[order(label.cex)] text(txt.layout[,1], txt.layout[,2], v.label, cex=label.cex, col=vertex.label.color) if (!is.null(leg)) { par(mar=c(0,0,0,0)) plot(0, axes = FALSE, pch = '') legend(x = 'center' , leg$unetoile, fill = leg$gcol) } dev.off() return(lo) } if (p.type=='tkplot') { id <- tkplot(g.toplot,vertex.label=v.label, edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color=vertex.label.color, edge.label=we.label, edge.color=edge.col, layout=lo) coords = tkplot.getcoords(id) ok <- try(coords <- tkplot.getcoords(id), TRUE) while (is.matrix(ok)) { ok <- try(coords <- tkplot.getcoords(id), TRUE) Sys.sleep(0.5) } tkplot.off() return(coords) } if (p.type == 'rgl' || p.type == 'rglweb') { library('rgl') #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) 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") movie3d(spin3d(axis=c(0,1,0),rpm=6), movie = 'film_graph', frames = "tmpfilm", duration=10, clean=TRUE, top = TRUE, dir = movie) ReturnVal <- tkmessageBox(title="RGL 3 D",message="Film fini !",icon="info",type="ok") } #play3d(spin3d(axis=c(0,1,0),rpm=6)) 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) } } graph.word <- function(mat.simi, index) { nm <- matrix(0, ncol = ncol(mat.simi), nrow=nrow(mat.simi), dimnames=list(row.names(mat.simi), colnames(mat.simi))) nm[,index] <- mat.simi[,index] 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) }