graph to file

diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R
index a00a186..4a23d3e 100644 (file)
--- a/Rscripts/Rgraph.R
+++ b/Rscripts/Rgraph.R
@@ -227,7 +227,7 @@ stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {
                        } else {
                                if(r>sqrt(.5)){
                                        print(paste(words[i], "could not be fit on page. It will not be plotted."))
                        } else {
                                if(r>sqrt(.5)){
                                        print(paste(words[i], "could not be fit on page. It will not be plotted."))

-                    notplot <- rbind(notplot,c(words[i], x[i,1], x[i,2]))
+                    notplot <- rbind(notplot,c(words[i], x[i,1], x[i,2], size[i], i))

                                        isOverlaped <- FALSE
                                }
                                theta <- theta+thetaStep
                                        isOverlaped <- FALSE
                                }
                                theta <- theta+thetaStep


@@ -419,8 +419,6 @@ select_point_chi <- function(tablechi, chi_limit) {
 select.chi.classe <- function(tablechi, nb, active = TRUE) {
     rowkeep <- NULL
     if (active & !is.null(debsup)) {
 select.chi.classe <- function(tablechi, nb, active = TRUE) {
     rowkeep <- NULL
     if (active & !is.null(debsup)) {

-        print(debsup)
-        print('###############################################################@')

         tablechi <- tablechi[1:(debsup-1),]
     }
     if (nb > nrow(tablechi)) {
         tablechi <- tablechi[1:(debsup-1),]
     }
     if (nb > nrow(tablechi)) {


@@ -433,6 +431,21 @@ select.chi.classe <- function(tablechi, nb, active = TRUE) {
     rowkeep
 }
 
     rowkeep
 }
 

+select.chi.classe.et <- function(tablechi, nb){
+    rowkeep <- NULL
+    if (!is.null(debet)) {
+        ntablechi <- tablechi[debet:nrow(tablechi),]
+    }
+    if (nb > nrow(ntablechi)) {
+        nb <- nrow(ntablechi)
+    }
+    for (i in 1:ncol(ntablechi)) {
+        rowkeep <- append(rowkeep,order(ntablechi[,i], decreasing = TRUE)[1:nb])
+    }
+    rowkeep <- unique(rowkeep)
+    rowkeep    
+}
+

 #from summary.ca
 summary.ca.dm <- function(object, scree = TRUE, ...){
   obj <- object
 #from summary.ca
 summary.ca.dm <- function(object, scree = TRUE, ...){
   obj <- object


@@ -621,6 +634,8 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro
     tree.order<- as.numeric(tree$tip.label)
        vec.mat<-NULL
     row.keep <- select.chi.classe(chisqtable, nbbycl)
     tree.order<- as.numeric(tree$tip.label)
        vec.mat<-NULL
     row.keep <- select.chi.classe(chisqtable, nbbycl)

+    #et.keep <- select.chi.classe.et(chisqtable, 10)
+    #print(chistable[et.keep,])

     toplot <- chisqtable[row.keep,]
     lclasses <- list()
     for (classe in 1:length(sum.cl)) {
     toplot <- chisqtable[row.keep,]
     lclasses <- list()
     for (classe in 1:length(sum.cl)) {


@@ -654,16 +669,16 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro
            tree[[2]]<-paste('classe ',tree[[2]])
     }
        par(mar=c(2,1,0,1))
            tree[[2]]<-paste('classe ',tree[[2]])
     }
        par(mar=c(2,1,0,1))

-       plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.4, y.lim=c(-0.3,tree$Nnode))
+       plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1, y.lim=c(-0.3,tree$Nnode))

        par(mar=c(0,0,0,0))
        d <- barplot(-sum.cl[tree.order], col=col, names.arg='', axes=FALSE, axisname=FALSE)
        par(mar=c(0,0,0,0))
        d <- barplot(-sum.cl[tree.order], col=col, names.arg='', axes=FALSE, axisname=FALSE)

-       text(x=d, y=(-sum.cl[tree.order]+3), label=paste(round(sum.cl[tree.order],1),'%'), cex=1.4)
+       text(x=d, y=(-sum.cl[tree.order]+3), label=paste(round(sum.cl[tree.order],1),'%'), cex=1)

     for (i in tree.order) {
         par(mar=c(0,0,1,0),cex=0.7)
         #wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(1.5, 0.2), random.order=FALSE, colors = colcloud[i])
         yval <- 1.1
         plot(0,0,pch='', axes = FALSE)
     for (i in tree.order) {
         par(mar=c(0,0,1,0),cex=0.7)
         #wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(1.5, 0.2), random.order=FALSE, colors = colcloud[i])
         yval <- 1.1
         plot(0,0,pch='', axes = FALSE)

-        vcex <- norm.vec(lclasses[[i]], 1, 2)
+        vcex <- norm.vec(lclasses[[i]], 1, 3)

         for (j in 1:length(lclasses[[i]])) {
             yval <- yval-(strheight( names(lclasses[[i]])[j],cex=vcex[j])+0.02)
             text(-0.9, yval, names(lclasses[[i]])[j], cex = vcex[j], col = colcloud[i], adj=0)
         for (j in 1:length(lclasses[[i]])) {
             yval <- yval-(strheight( names(lclasses[[i]])[j],cex=vcex[j])+0.02)
             text(-0.9, yval, names(lclasses[[i]])[j], cex = vcex[j], col = colcloud[i], adj=0)


@@ -795,7 +810,7 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f
 }
 #tree <- tree.cut1$tree.cl
 #to.plot <- di
 }
 #tree <- tree.cut1$tree.cl
 #to.plot <- di

-plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), colbar=NULL, classes=NULL, cmd=FALSE) {
+plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), colbar=NULL, classes=NULL, direction = 'rightwards', cmd=FALSE) {

     tree.order<- as.numeric(tree$tip.label)
        if (!is.null(classes)) {
                classes<-classes[classes!=0]
     tree.order<- as.numeric(tree$tip.label)
        if (!is.null(classes)) {
                classes<-classes[classes!=0]


@@ -806,12 +821,27 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2
                sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
        }
     par(mar=c(0,0,0,0))
                sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
        }
     par(mar=c(0,0,0,0))

-       if (!is.null(classes)) {
-               matlay <- matrix(c(1,2,3,4),1,byrow=TRUE)
-               lay.width <- c(3,2,3,2)
-       } else {
-               matlay <- matrix(c(1,2,3),1,byrow=TRUE)
-       }
+    if (direction == 'rightwards') {
+        srt <- 0
+        adj <- NULL
+        horiz <- TRUE
+           if (!is.null(classes)) {
+                   matlay <- matrix(c(1,2,3,4),1,byrow=TRUE)
+                   lay.width <- c(3,2,3,2)
+           } else {
+                   matlay <- matrix(c(1,2,3),1,byrow=TRUE)
+           }
+    } else {
+        srt <- 90
+        adj <- 0.5
+        horiz <- FALSE
+        if (!is.null(classes)) {
+            matlay <- matrix(c(1,2,3,4,4,4),3)
+        } else {
+            matlay <- matrix(c(1,2,3,3),2)
+        }
+        lay.width <- c(5,2)
+    }

     layout(matlay, widths=lay.width,TRUE)
        par(mar=c(3,0,2,4),cex=1)
        label.ori<-tree[[2]]
     layout(matlay, widths=lay.width,TRUE)
        par(mar=c(3,0,2,4),cex=1)
        label.ori<-tree[[2]]


@@ -835,7 +865,7 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2
         col.bars <- grey.colors(nrow(to.plot),0,0.8)
     }
     col <- col[tree.order]
         col.bars <- grey.colors(nrow(to.plot),0,0.8)
     }
     col <- col[tree.order]

-       plot.phylo(tree,label.offset=0.2,tip.col=col)
+       plot.phylo(tree,label.offset=0.2,tip.col=col, direction = direction, srt=srt, adj = 0.5, edge.width = 2)

        if (!is.null(classes)) {
                par(cex=0.7)
                par(mar=c(3,0,2,1))
        if (!is.null(classes)) {
                par(cex=0.7)
                par(mar=c(3,0,2,1))


@@ -844,7 +874,7 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2
                text(x=to.plota, y=d[,1], label=paste(round(to.plota,1),'%'), adj=1.2)
        }
     par(mar=c(3,0,2,1))
                text(x=to.plota, y=d[,1], label=paste(round(to.plota,1),'%'), adj=1.2)
        }
     par(mar=c(3,0,2,1))

-    d <- barplot(to.plot,horiz=TRUE, col=col.bars, beside=TRUE, names.arg='', space = c(0.1,0.6), axisname=FALSE)
+    d <- barplot(to.plot,horiz=horiz, col=col.bars, beside=TRUE, names.arg='', space = c(0.1,0.6), axisname=FALSE)

     c <- colMeans(d)
     c1 <- c[-1]
     c2 <- c[-length(c)]
     c <- colMeans(d)
     c1 <- c[-1]
     c2 <- c[-length(c)]


@@ -1085,23 +1115,36 @@ simi.to.gexf <- function(fileout, graph.simi, nodes.attr = NULL) {
        g <- graph.simi$graph
        nodes <- data.frame(cbind(1:nrow(lo), V(g)$name))
        colnames(nodes) <- c('id', 'label')
        g <- graph.simi$graph
        nodes <- data.frame(cbind(1:nrow(lo), V(g)$name))
        colnames(nodes) <- c('id', 'label')

-       print(nodes)

        if (! is.null(nodes.attr)) {
                nodesatt <- as.data.frame(nodes.attr)
        } else {
                nodesatt <- data.frame(cbind(lo[,1],lo[,2]))
        }
        edges <- as.data.frame(get.edges(g, c(1:ecount(g))))
        if (! is.null(nodes.attr)) {
                nodesatt <- as.data.frame(nodes.attr)
        } else {
                nodesatt <- data.frame(cbind(lo[,1],lo[,2]))
        }
        edges <- as.data.frame(get.edges(g, c(1:ecount(g))))

-       col <- rep('red', nrow(lo))
+       col <- graph.simi$color

        col <- t(sapply(col, col2rgb, alpha=TRUE))
        col <- t(sapply(col, col2rgb, alpha=TRUE))

-       write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo))
+       write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo, size=graph.simi$label.cex), edgesVizAtt=list(size=graph.simi$we.width))
+}
+
+graphml.to.file <- function(graph.path) {
+    library(igraph)
+    g <- read.graph(graph.path, format='graphml')
+    layout <- layout.fruchterman.reingold(g, dim=3)
+    #print(V(g)$color)
+    graph.simi <- list(graph=g, layout=layout, color = V(g)$color ,eff=V(g)$weight)
+    graph.simi

 }
 
 
 }
 
 

-graph.to.file <- function(grah.simi, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
+graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {

        require(igraph)
        g <- graph.simi$graph
        require(igraph)
        g <- graph.simi$graph

-       V(g)$weight <- graph.simi$eff
+    print(graph.simi$eff)
+    if (!is.null(graph.simi$eff)) {
+           V(g)$weight <- graph.simi$eff
+    } else {
+        V(g)$weight <- graph.simi$label.cex
+    }

        V(g)$x <- graph.simi$layout[,1]
        V(g)$y <- graph.simi$layout[,2]
        if (ncol(graph.simi$layout) == 3) {
        V(g)$x <- graph.simi$layout[,1]
        V(g)$y <- graph.simi$layout[,2]
        if (ncol(graph.simi$layout) == 3) {


@@ -1127,10 +1170,10 @@ graph.to.file <- function(grah.simi, nodesfile = NULL, edgesfile = NULL, communi
        }
        df <- get.data.frame(g, what='both')
        if (!is.null(nodesfile)) {
        }
        df <- get.data.frame(g, what='both')
        if (!is.null(nodesfile)) {

-               write.table(df$vertices, nodesfile, sep='\t')
+               write.table(df$vertices, nodesfile, sep='\t', row.names=FALSE)

        }
        if (!is.null(edgesfile)) {
        }
        if (!is.null(edgesfile)) {

-               write.table(df$edges, edgesfile, sep='\t')
+               write.table(df$edges, edgesfile, sep='\t', row.names=FALSE)

        }
        if (is.null(edgesfile) & is.null(nodesfile)) {
                df
        }
        if (is.null(edgesfile) & is.null(nodesfile)) {
                df