X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=Rscripts%2FRgraph.R;h=12938bf95c6decdcfb0a317d383d6c4d232a4123;hp=39fe61839b1585d5e683f161e36a5e529a804e5b;hb=9ae220065c6a29fa4fa4f24a3269631e902c228d;hpb=54fef96ad151ba25920f3e589b39a83c3f62ae2c

diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R
index 39fe618..12938bf 100644
--- a/Rscripts/Rgraph.R
+++ b/Rscripts/Rgraph.R
@@ -107,7 +107,7 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto
     classes <- classes[order(cex.par, decreasing = TRUE)]
     cex.par <- cex.par[order(cex.par, decreasing = TRUE)]
     table.out <- stopoverlap(table.in, cex.par=cex.par, xlim = c(xmin,xmax), ylim = c(ymin,ymax))
-    table.in <- table.out$toplot
+	table.in <- table.out$toplot
     notplot <- table.out$notplot
     if (! is.null(notplot)) {
         write.csv2(notplot, file = paste(filename, '_notplotted.csv', sep = ''))
@@ -226,8 +226,8 @@ stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {
 				isOverlaped <- FALSE
 			} 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]))
+					#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], size[i], i))
 					isOverlaped <- FALSE
 				}
 				theta <- theta+thetaStep
@@ -237,6 +237,8 @@ stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {
 			}
 		}
     }
+	nbnot <- nrow(notplot)
+	print(paste(nbnot, ' not plotted'))
     row.names(toplot) <- words[toplot[,4]]
     return(list(toplot = toplot, notplot = notplot))
 }
@@ -343,6 +345,19 @@ getwordcloudcoord <- function(words,freq,scale=c(4,.5),min.freq=3,max.words=Inf,
 	return(toplot)
 }
 
+new_tree_tot <- function(chd) {
+	lf <- chd$list_fille
+	m <- matrix(0, ncol=2)
+	for (val in 1:length(lf)) {
+		if (! is.null(lf[[val]])) {
+			print(c(val,lf[[val]][1]))
+			m <- rbind(m, c(val,lf[[val]][1]))
+			m <- rbind(m, c(val,lf[[val]][2]))
+		}
+	}
+	m[-1,]
+}
+
 make_tree_tot <- function (chd) {
 	library(ape)
 	lf<-chd$list_fille
@@ -419,8 +434,6 @@ select_point_chi <- function(tablechi, chi_limit) {
 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)) {
@@ -433,6 +446,21 @@ select.chi.classe <- function(tablechi, nb, active = TRUE) {
     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
@@ -559,7 +587,7 @@ del.yellow <- function(colors) {
     tochange <- apply(rgbs, 2, is.yellow)
     tochange <- which(tochange)
     if (length(tochange)) {
-        gr.col <- grey.colors(length(tochange), start = 0.5)
+        gr.col <- grey.colors(length(tochange), start = 0.5, end = 0.8)
     }
     compt <- 1
     for (val in tochange) {
@@ -569,30 +597,34 @@ del.yellow <- function(colors) {
     colors
 }
 
-make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) {
+make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL, color=NULL) {
     
     rain <- rainbow(clnb)
     compt <- 1
     tochange <- NULL
-    for (my.color in rain) {
-        my.color <- col2rgb(my.color)
-        if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
-           tochange <- append(tochange, compt)   
-        }
-        compt <- compt + 1
-    }
-    if (!is.null(tochange)) {
-        gr.col <- grey.colors(length(tochange))
-        compt <- 1
-        for (val in tochange) {
-            rain[val] <- gr.col[compt]
-            compt <- compt + 1
-        }
-    }
-	cl.color <- rain[classes]
+    #for (my.color in rain) {
+    #    my.color <- col2rgb(my.color)
+    #    if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
+    #       tochange <- append(tochange, compt)   
+    #    }
+    #    compt <- compt + 1
+    #}
+    #if (!is.null(tochange)) {
+    #    gr.col <- grey.colors(length(tochange))
+    #    compt <- 1
+    #    for (val in tochange) {
+    #        rain[val] <- gr.col[compt]
+    #        compt <- compt + 1
+    #    }
+    #}
+	rain <- del.yellow(rain)
+    cl.color <- rain[classes]
     if (black) {
         cl.color <- 'black'
     }
+    if (!is.null(color)) {
+        cl.color <- color
+    }
 	plot(toplot[,1],toplot[,2], pch='', xlab = xlab, ylab = ylab, xlim=xminmax, ylim = yminmax)
 	abline(h=0, v=0, lty = 'dashed')
 	if (is.null(cex.txt))
@@ -620,6 +652,8 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro
     tree.order<- as.numeric(tree$tip.label)
 	vec.mat<-NULL
     row.keep <- select.chi.classe(chisqtable, nbbycl)
+    #et.keep <- select.chi.classe.et(chisqtable, 10)
+    #print(chistable[et.keep,])
     toplot <- chisqtable[row.keep,]
     lclasses <- list()
     for (classe in 1:length(sum.cl)) {
@@ -627,7 +661,10 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro
        names(ntoplot) <- rownames(toplot)
        ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
        ntoplot <- round(ntoplot, 0)
-       ntoplot <- ntoplot[1:nbbycl]
+       if (length(toplot) > nbbycl) {
+           ntoplot <- ntoplot[1:nbbycl]
+       }       
+       ntoplot <- ntoplot[which(ntoplot > 0)]
        #ntoplot <- ntoplot[order(ntoplot)]
        #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
        lclasses[[classe]] <- ntoplot
@@ -637,8 +674,9 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro
     vec.mat[3,] <- 3:(length(sum.cl)+2)
     layout(matrix(vec.mat, nrow=3, ncol=length(sum.cl)),heights=c(2,1,6))
     if (! bw) {
-        col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+        col <- rainbow(length(sum.cl))
         col <- del.yellow(col)
+        col <- col[as.numeric(tree$tip.label)]
         colcloud <- rainbow(length(sum.cl))
         colcloud <- del.yellow(colcloud)
     }
@@ -649,21 +687,24 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro
 	    tree[[2]]<-paste('classe ',tree[[2]])
     }
 	par(mar=c(2,1,0,1))
-	plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.4, y.lim=c(-0.3,tree$Nnode))
+	plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.5, 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)
-	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)
-        vcex <- norm.vec(lclasses[[i]], 1.5, 2.5)
+        vcex <- norm.vec(lclasses[[i]], 2, 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)
         }
     }
+    if (!from.cmd) {
+        dev.off()
+    }
     
 }
 
@@ -684,10 +725,14 @@ plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendr
     lclasses <- list()
     for (classe in 1:length(sum.cl)) {
        ntoplot <- toplot[,classe]
+       names(ntoplot) <- rownames(toplot)
        ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
        ntoplot <- round(ntoplot, 0)
-       ntoplot <- ntoplot[1:nbbycl]
+       if (length(toplot) > nbbycl) {
+            ntoplot <- ntoplot[1:nbbycl]
+       }
        ntoplot <- ntoplot[order(ntoplot)]
+       ntoplot <- ntoplot[which(ntoplot > 0)]
        #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
        lclasses[[classe]] <- ntoplot
     }
@@ -712,7 +757,7 @@ plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendr
 	plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
     for (i in rev(tree.order)) {
         par(mar=c(0,0,1,0),cex=0.9)
-        wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(4, 0.8), random.order=FALSE, colors = colcloud[i])
+        wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(2.5, 0.5), random.order=FALSE, colors = colcloud[i])
     }
 }
 
@@ -754,11 +799,11 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f
         }
     }
 	par(mar=c(0,0,0,0),cex=1)
-	label.ori<-tree[[2]]
+	label.ori<-tree$tip.label
     if (!is.null(lab)) {
         tree$tip.label <- lab
     } else {
-	    tree[[2]]<-paste('classe ',tree[[2]])
+	    tree$tip.label<-paste('classe ',tree$tip.label)
     }
 	plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
     #cl.order <- as.numeric(label.ori)
@@ -783,7 +828,7 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f
 }
 #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]
@@ -794,17 +839,32 @@ 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))
-	if (!is.null(classes)) {
-		matlay <- matrix(c(1,2,3,4),1,byrow=TRUE)
-		lay.width <- c(3,1,3,2)
-	} 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(3,0,2,0),cex=1)
+	par(mar=c(3,0,2,4),cex=1)
 	label.ori<-tree[[2]]
     if (!is.null(lab)) {
-        tree$tip.label <- lab
+        tree$tip.label <- lab[tree.order]
     } else {
 	    tree[[2]]<-paste('classe ',tree[[2]])
     }
@@ -823,7 +883,7 @@ 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]
-	plot.phylo(tree,label.offset=0.1,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))
@@ -832,7 +892,7 @@ 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))
-    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)]
@@ -858,7 +918,7 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2
     }    
     par(mar=c(0,0,0,0))
     plot(0, axes = FALSE, pch = '')
-    legend(x = 'center' , rownames(to.plot), fill = col.bars)
+    legend(x = 'center' , rev(rownames(to.plot)), fill = rev(col.bars))
     if (!cmd) {
         dev.off()
     }
@@ -1073,27 +1133,43 @@ 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')
-	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))))
-	col <- rep('red', nrow(lo))
+	col <- graph.simi$color
 	col <- t(sapply(col, col2rgb, alpha=TRUE))
-	write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo))
+	write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo, size=graph.simi$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$graph
-	V(g)$weight <- graph.simi$eff
-	V(g)$x <- graph.simi$layout[,1]
-	V(g)$y <- graph.simi$layout[,2]
-	if (ncol(graph.simi$layout) == 3) {
-		V(g)$z <- graph.simi$layout[,3]
+    print(graph.simi$eff)
+    if (!is.null(graph.simi$eff)) {
+	    V(g)$weight <- graph.simi$eff
+    } else {
+        V(g)$weight <- graph.simi$label.cex
+    }
+	layout <- layout.norm(graph.simi$layout,-5,5,-5,5,-5,5)
+	print(layout)
+	V(g)$x <- layout[,1]
+	V(g)$y <- layout[,2]
+	if (ncol(layout) == 3) {
+		V(g)$z <- layout[,3]
 	}
 	if (community) {
 		member <- graph.simi$communities$membership
@@ -1115,12 +1191,48 @@ graph.to.file <- function(grah.simi, nodesfile = NULL, edgesfile = NULL, communi
 	}
 	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)) {
+		write.table(df$edges, edgesfile, sep='\t', row.names=FALSE)
+	}
+	if (is.null(edgesfile) & is.null(nodesfile)) {
+		df
+	}
+}
+
+graph.to.file2 <- function(graph, layout, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
+	require(igraph)
+	g <- graph
+	V(g)$x <- layout[,1]
+	V(g)$y <- layout[,2]
+	if (ncol(layout) == 3) {
+		V(g)$z <- layout[,3]
+	}
+	v.colors <- col2rgb(V(g)$color)
+	V(g)$r <- v.colors[1,]
+	V(g)$g <- v.colors[2,]
+	V(g)$b <- v.colors[3,]		
+	
+	if (!is.null(sweight)) {
+		V(g)$sweight <- sweight
+	}
+	if (is.null(V(g)$weight)) {
+		if (!is.null(sweight)) {
+			V(g)$weight <- sweight
+		} else {
+			V(g)$weight <- 1
+		}
+	}
+	df <- get.data.frame(g, what='both')
+	if (!is.null(nodesfile)) {
+		write.table(df$vertices, nodesfile, sep='\t', row.names=FALSE)
 	}
 	if (!is.null(edgesfile)) {
-		write.table(df$edges, edgesfile, sep='\t')
+		write.table(df$edges, edgesfile, sep='\t', row.names=FALSE)
 	}
 	if (is.null(edgesfile) & is.null(nodesfile)) {
 		df
 	}
 }
+