# dev.off()
#}
-PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=900, height=900, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL, xmin=NULL, xmax=NULL, ymin=NULL, ymax=NULL) {
+PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=900, height=900, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL, xmin=NULL, xmax=NULL, ymin=NULL, ymax=NULL, active = TRUE) {
if (col) {
if (what == 'coord') {
rowcoord <- as.matrix(afc$colcoord)
if (!col) {
classes <- as.matrix(apply(chitable,1,which.max))
cex.par <- norm.vec(apply(chitable,1,max), 0.8,3)
- row.keep <- select.chi.classe(chitable, 80)
+ row.keep <- select.chi.classe(chitable, 80, active=active)
rowcoord <- rowcoord[row.keep,]
classes <- classes[row.keep]
cex.par <- cex.par[row.keep]
svg(filename.to.svg(filename), width=width, height=height)
}
} else {
- #library(RSvgDevice)
if (svg) {
svg(filename.to.svg(filename), width=width/74.97, height=height/74.97)
} else {
row_keep
}
-select.chi.classe <- function(tablechi, nb) {
+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)) {
nb <- nrow(tablechi)
}
res
}
+is.yellow <- function(my.color) {
+ if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
+ return(TRUE)
+ } else {
+ return(FALSE)
+ }
+}
+
+del.yellow <- function(colors) {
+ rgbs <- col2rgb(colors)
+ tochange <- apply(rgbs, 2, is.yellow)
+ tochange <- which(tochange)
+ if (length(tochange)) {
+ gr.col <- grey.colors(length(tochange))
+ }
+ compt <- 1
+ for (val in tochange) {
+ colors[val] <- gr.col[compt]
+ compt <- compt + 1
+ }
+ colors
+}
+
make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) {
rain <- rainbow(clnb)
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]
#ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
lclasses[[classe]] <- ntoplot
}
- vec.mat <- matrix(1, nrow = 2, ncol = length(sum.cl))
- vec.mat[2,] <- 2:(length(sum.cl)+1)
- layout(matrix(vec.mat, nrow=2, ncol=length(sum.cl)),heights=c(1,4))
+ vec.mat <- matrix(1, nrow = 3, ncol = length(sum.cl))
+ vec.mat[2,] <- 2
+ vec.mat[3,] <- 3:(length(sum.cl)+2)
+ layout(matrix(vec.mat, nrow=3, ncol=length(sum.cl)),heights=c(1,1,6))
if (! bw) {
col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+ col <- del.yellow(col)
colcloud <- rainbow(length(sum.cl))
+ colcloud <- del.yellow(colcloud)
}
- par(mar=c(1,0,0,0))
label.ori<-tree[[2]]
if (!is.null(lab)) {
tree$tip.label <- lab
} else {
tree[[2]]<-paste('classe ',tree[[2]])
}
- plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0)
+ par(mar=c(1,1,0,1))
+ plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.4, y.lim=c(-0.3,tree$Nnode))
+ 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)
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]], 0.8, 3)
+ vcex <- norm.vec(lclasses[[i]], 1.5, 2.5)
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 (! bw) {
col <- rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)]
+ col <- del.yellow(col)
col.bars <- col
col.pie <- rainbow(nrow(sum.cl))
+ col.pie <- del.yellow(col.pie)
#col.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])]
} else {
col = 'black'
}
#tree <- tree.cut1$tree.cl
#to.plot <- di
-plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), cmd=FALSE) {
+plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), colbar=NULL, classes=NULL, cmd=FALSE) {
tree.order<- as.numeric(tree$tip.label)
+ if (!is.null(classes)) {
+ classes<-classes[classes!=0]
+ classes<-as.factor(classes)
+ sum.cl<-as.matrix(summary(classes, maxsum=1000000))
+ sum.cl<-(sum.cl/colSums(sum.cl)*100)
+ sum.cl<-round(sum.cl,2)
+ sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
+ }
par(mar=c(0,0,0,0))
- layout(matrix(c(1,2,3),1,byrow=TRUE), widths=lay.width,TRUE)
+ if (!is.null(classes)) {
+ matlay <- matrix(c(1,2,3,4),1,byrow=TRUE)
+ lay.width <- c(3,1,3,2)
+ } else {
+ matlay <- matrix(c(1,2,3),1,byrow=TRUE)
+ }
+ layout(matlay, widths=lay.width,TRUE)
par(mar=c(3,0,2,0),cex=1)
label.ori<-tree[[2]]
if (!is.null(lab)) {
}
to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot)))
if (!bw) {
- col <- rainbow(ncol(to.plot))
- col.bars <- rainbow(nrow(to.plot))
+ col <- rainbow(ncol(to.plot))
+ col <- del.yellow(col)
+ if (is.null(colbar)) {
+ col.bars <- rainbow(nrow(to.plot))
+ col.bars <- del.yellow(col.bars)
+ } else {
+ col.bars <- colbar
+ }
} else {
col <- 'black'
col.bars <- grey.colors(nrow(to.plot),0,0.8)
}
col <- col[tree.order]
plot.phylo(tree,label.offset=0.1,tip.col=col)
-
+ if (!is.null(classes)) {
+ par(cex=0.7)
+ par(mar=c(3,0,2,1))
+ to.plota <- sum.cl[tree.order,1]
+ d <- barplot(to.plota,horiz=TRUE, col=col, names.arg='', axes=FALSE, axisname=FALSE)
+ text(x=to.plota, y=d[,1], label=paste(round(to.plota,1),'%'), adj=1.2)
+ }
par(mar=c(3,0,2,1))
d <- barplot(to.plot,horiz=TRUE, col=col.bars, beside=TRUE, names.arg='', space = c(0.1,0.6), axisname=FALSE)
c <- colMeans(d)
#d <- barplot(to.plot,horiz=TRUE, names.arg='', axes=FALSE, axisname=FALSE)
#text(x=to.plot, y=d[,1], label=round(to.plot,1), adj=1.2)
+make.afc.attributes <- function(rn, afc.table, contafc, clnb, column = FALSE, x=1, y=2) {
+ if (!column){
+ nd <- clnb - 1
+ afc.res <- afc.table$ligne
+ #tokeep <- which(row.names(afc.res) %in% rn)
+ afc.res <- afc.res[rn,]
+ debcor <- (nd*2) + 1
+ cor <- afc.res[,debcor:(debcor+nd-1)][,c(x,y)]
+ debctr <- (nd*3) + 1
+ ctr <- afc.res[,debctr:(debctr+nd-1)][,c(x,y)]
+ massdeb <- (nd*4) + 1
+ mass <- afc.res[,massdeb]
+ chideb <- massdeb + 1
+ chi <- afc.res[,chideb]
+ inertiadeb <- chideb + 1
+ inertia <- afc.res[,inertiadeb]
+ frequence <- rowSums(contafc[rn,])
+ }
+ res <- list(frequence=frequence, cor, ctr, mass = mass, chi=chi, inertia=inertia)
+ return(res)
+}
+
+
+afctogexf <- function(fileout, toplot, classes, clnb, sizes, nodes.attr=NULL) {
+ toplot <- toplot[,1:3]
+ toplot[,3] <- 0
+ #toplot <- afc$rowcoord[1:100,1:3]
+ #toplot[,3] <- 0
+ #rownames(toplot)<-afc$rownames[1:100]
+ cc <- rainbow(clnb)[classes]
+ cc <- t(sapply(cc, col2rgb, alpha=TRUE))
+ #sizes <- apply(chistabletot[1:100,], 1, max)
+
+ nodes <- data.frame(cbind(1:nrow(toplot), rownames(toplot)))
+ colnames(nodes) <- c('id', 'label')
+ nodes[,1] <- as.character(nodes[,1])
+ nodes[,2] <- as.character(nodes[,2])
+ #nodes attributs
+ if (! is.null(nodes.attr)) {
+ nodesatt <- as.data.frame(nodes.attr)
+ } else {
+ nodesatt <- data.frame(cbind(toplot[,1],toplot[,2]))
+ }
+ #make axes
+ edges<-matrix(c(1,1),ncol=2)
+ xmin <- min(toplot[,1])
+ xmax <- max(toplot[,1])
+ ymin <- min(toplot[,2])
+ ymax <- max(toplot[,2])
+ nodes<-rbind(nodes, c(nrow(nodes)+1, 'F1'))
+ nodes<-rbind(nodes, c(nrow(nodes)+1, 'F1'))
+ nodes<-rbind(nodes, c(nrow(nodes)+1, 'F2'))
+ nodes<-rbind(nodes, c(nrow(nodes)+1, 'F2'))
+ nodesatt<-rbind(nodesatt, c(0,0))
+ nodesatt<-rbind(nodesatt, c(0,0))
+ nodesatt<-rbind(nodesatt, c(0,0))
+ nodesatt<-rbind(nodesatt, c(0,0))
+ toplot <- rbind(toplot, c(xmin, 0,0))
+ toplot <- rbind(toplot, c(xmax,0,0))
+ toplot <- rbind(toplot, c(0,ymin,0))
+ toplot <- rbind(toplot, c(0,ymax,0))
+ cc <- rbind(cc, c(255,255,255,1))
+ cc <- rbind(cc, c(255,255,255,1))
+ cc <- rbind(cc, c(255,255,255,1))
+ cc <- rbind(cc, c(255,255,255,1))
+ sizes <- c(sizes, c(0.5, 0.5, 0.5, 0.5))
+ edges <- rbind(edges, c(nrow(nodes)-3, nrow(nodes)-2))
+ edges <- rbind(edges, c(nrow(nodes)-1, nrow(nodes)))
+ write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=cc, position=toplot, size=sizes))
+}
+
+simi.to.gexf <- function(fileout, graph.simi, nodes.attr = NULL) {
+ lo <- graph.simi$layout
+ if (ncol(lo) == 3) {
+ lo[,3] <- 0
+ } else {
+ lo <- cbind(lo, rep(0,nrow(lo)))
+ }
+ g <- graph.simi$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 <- t(sapply(col, col2rgb, alpha=TRUE))
+ write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo))
+}
projects / iramuteq / commitdiff