correction for wordcloud >= 2.6

[iramuteq] / Rscripts / Rgraph.R

diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R
index dacd7a8..af0b351 100644 (file)
--- a/Rscripts/Rgraph.R
+++ b/Rscripts/Rgraph.R
@@ -183,7 +183,11 @@ overlap <- function(x1, y1, sw1, sh1, boxes) {
 }
 
 .overlap <- function(x11,y11,sw11,sh11,boxes1){
-    .Call("is_overlap",x11,y11,sw11,sh11,boxes1)
+       if (as.character(packageVersion('wordcloud')) >= '2.6') {
+               .Call("_wordcloud_is_overlap", x11,y11,sw11,sh11,boxes1)
+       } else {
+               .Call("is_overlap",x11,y11,sw11,sh11,boxes1)
+       }
 }
 ########################################################
 stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {
@@ -680,12 +684,12 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro
         colcloud <- rainbow(length(sum.cl))
         colcloud <- del.yellow(colcloud)
     }
-    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)
+       }
        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 = 1.5, y.lim=c(-0.3,tree$Nnode))
        par(mar=c(0,0,0,0))
@@ -748,12 +752,12 @@ plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendr
         colcloud <- rainbow(length(sum.cl))
     }
     par(mar=c(0,0,0,0))
-    label.ori<-tree[[2]]
+       label.ori<-tree$tip.label
     if (!is.null(lab)) {
         tree$tip.label <- lab
     } else {
-           tree[[2]]<-paste('classe ',tree[[2]])
-    }
+           tree$tip.label<-paste('classe ',tree$tip.label)
+       }
        plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
     for (i in rev(tree.order)) {
         par(mar=c(0,0,1,0),cex=0.9)
@@ -799,11 +803,11 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f
         }
     }
        par(mar=c(0,0,0,0),cex=1)
-       label.ori<-tree[[2]]
+       label.ori<-tree$tip.label
     if (!is.null(lab)) {
         tree$tip.label <- lab
     } else {
-           tree[[2]]<-paste('classe ',tree[[2]])
+           tree$tip.label<-paste('classe ',tree$tip.label)
     }
        plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
     #cl.order <- as.numeric(label.ori)
@@ -862,11 +866,11 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2
     }
     layout(matlay, widths=lay.width,TRUE)
        par(mar=c(3,0,2,4),cex=1)
-       label.ori<-tree[[2]]
+       label.ori<-tree$tip.label
     if (!is.null(lab)) {
-        tree$tip.label <- lab[tree.order]
+        tree$tip.label <- lab
     } else {
-           tree[[2]]<-paste('classe ',tree[[2]])
+           tree$tip.label<-paste('classe ',tree$tip.label)
     }
     to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot)))
     if (!bw) {
@@ -925,6 +929,36 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2
        tree[[2]]<-label.ori
 }
 
+plot.spec <- function(spec, nb.word = 20) {
+       word.to.plot <- NULL
+       word.size <- NULL
+       rno <- rownames(spec)
+       cn <- colnames(spec)
+       if (nb.word > length(rno)) {nb.word <- length(rno)}
+       for (val in 1:ncol(spec)) {
+               rn <- rno[order(spec[,val], decreasing=T)][1:nb.word]
+               score <- spec[order(spec[,val], decreasing=T),val][1:nb.word]
+               word.to.plot <- cbind(word.to.plot, rn)
+               word.size <- cbind(word.size, score)
+       }
+       mat.lay <- matrix(1:ncol(spec),nrow=1,ncol=ncol(spec))
+       layout(mat.lay)
+       for (i in 1:ncol(spec)) {
+               col <- ifelse((i %% 2) == 0, 'red', 'blue')
+               par(mar=c(0,0,1,0),cex=0.7)
+           yval <- 1.1
+           plot(0,0,pch='', axes = FALSE)
+           vcex <- norm.vec(word.size[,i], 2, 3)
+               text(-0.9, -0.5, cn[i], cex = 1, adj=0, srt=90, col='black')
+           for (j in 1:length(word.size[,i])) {
+               yval <- yval-(strheight(word.to.plot[j,i],cex=vcex[j])+0.02)
+               text(-0.9, yval, word.to.plot[j,i], cex = vcex[j], col = col, adj=0)
+           }
+       }
+
+
+}
+
 plot.alceste.graph <- function(rdata,nd=3,layout='fruke', chilim = 2) {
     load(rdata)
     if (is.null(debsup)) {
@@ -1164,10 +1198,12 @@ graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, commun
     } 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$layout) == 3) {
-               V(g)$z <- graph.simi$layout[,3]
+       layout <- layout.norm(graph.simi$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$membership
@@ -1215,6 +1251,13 @@ graph.to.file2 <- function(graph, layout, nodesfile = NULL, edgesfile = NULL, co
        if (!is.null(sweight)) {
                V(g)$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)