X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=Rscripts%2Fsimi.R;h=b8c23692fb6d7a8c73b6c12a48d4fb022a9685bb;hp=98bacf7a50c3db6ac68d39a006704ed139f5a4e1;hb=12b4b71c8c8feb6154abc04dfa9bb93a521ef789;hpb=1f82fb8e9ed83b8524b00039f1a8c51c2b12a8be diff --git a/Rscripts/simi.R b/Rscripts/simi.R index 98bacf7..b8c2369 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) @@ -122,7 +122,11 @@ 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 { + + } E(g1)$weight<-invw g.max<-minimum.spanning.tree(g1) E(g.max)$weight<-1/E(g.max)$weight @@ -130,19 +134,20 @@ do.simi <- function(x, method = 'cooc',seuil = NULL, p.type = 'tkplot',layout.ty } if (!is.null(seuil)) { - if (seuil >= max(mat.simi)) seuil <- max(mat.simi)-1 + print(seuil) + if (seuil >= max(mat.simi)) seuil <- 0 vec<-vector() w<-E(g.toplot)$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 +192,32 @@ 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$graph if (is.null(vertex.size)) { @@ -232,14 +259,31 @@ plot.simi <- function(graph.simi, p.type = 'tkplot',filename=NULL, vertex.col = } if (p.type=='nplot') { #print('ATTENTION - PAS OPEN FILE') - open_file_graph(filename, width = width, height = height) + open_file_graph(filename, width = width, height = height, svg = svg) par(mar=c(2,2,2,2)) if (!is.null(leg)) { layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7))) par(mar=c(2,2,1,0)) } par(pch=' ') - plot(g.toplot,vertex.label='', edge.width=we.width, vertex.size=vertex.size, vertex.color=vertex.col, vertex.label.color='white', edge.label=we.label, edge.label.cex=cex, edge.color=edge.col, vertex.label.cex = 0, layout=lo)#, rescale = FALSE) + if (is.null(graph.simi$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)#, 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),] @@ -297,4 +341,9 @@ graph.word <- function(mat.simi, index) { 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 }