############FIXME##################
-PlotDendroComp <- function(chd,filename,reso) {
- jpeg(filename,res=reso)
- par(cex=PARCEX)
- plot(chd,which.plots=2, hang=-1)
- dev.off()
-}
-
-PlotDendroHori <- function(dendrocutupper,filename,reso) {
- jpeg(filename,res=reso)
- par(cex=PARCEX)
- nP <- list(col=3:2, cex=c(0.5, 0.75), pch= 21:22, bg= c('light blue', 'pink'),lab.cex = 0.75, lab.col = 'tomato')
- plot(dendrocutupper,nodePar= nP, edgePar = list(col='gray', lwd=2),horiz=TRUE, center=FALSE)
- dev.off()
-}
+#PlotDendroComp <- function(chd,filename,reso) {
+# jpeg(filename,res=reso)
+# par(cex=PARCEX)
+# plot(chd,which.plots=2, hang=-1)
+# dev.off()
+#}
+#
+#PlotDendroHori <- function(dendrocutupper,filename,reso) {
+# jpeg(filename,res=reso)
+# par(cex=PARCEX)
+# nP <- list(col=3:2, cex=c(0.5, 0.75), pch= 21:22, bg= c('light blue', 'pink'),lab.cex = 0.75, lab.col = 'tomato')
+# plot(dendrocutupper,nodePar= nP, edgePar = list(col='gray', lwd=2),horiz=TRUE, center=FALSE)
+# dev.off()
+#}
PlotDendroCut <- function(chd,filename,reso,clusternb) {
h.chd <- as.hclust(chd)
dev.off()
}
-PlotAfc<- function(afc, filename, width=800, height=800, quality=100, reso=200, toplot=c('all','all'), PARCEX=PARCEX) {
- if (Sys.info()["sysname"]=='Darwin') {
- width<-width/74.97
- height<-height/74.97
- quartz(file=filename,type='jpeg',width=width,height=height)
- } else {
- jpeg(filename,width=width,height=height,quality=quality,res=reso)
- }
- par(cex=PARCEX)
- plot(afc,what=toplot,labels=c(1,1),contrib=c('absolute','relative'))
- dev.off()
-}
-
-PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=800, height=800, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL) {
+#PlotAfc<- function(afc, filename, width=800, height=800, quality=100, reso=200, toplot=c('all','all'), PARCEX=PARCEX) {
+# if (Sys.info()["sysname"]=='Darwin') {
+# width<-width/74.97
+# height<-height/74.97
+# quartz(file=filename,type='jpeg',width=width,height=height)
+# } else {
+# jpeg(filename,width=width,height=height,quality=quality,res=reso)
+# }
+# par(cex=PARCEX)
+# plot(afc,what=toplot,labels=c(1,1),contrib=c('absolute','relative'))
+# 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=NUL) {
if (col) {
if (what == 'coord') {
rowcoord <- as.matrix(afc$colcoord)
}
x <- axetoplot[1]
y <- axetoplot[2]
-
if (col)
rownames(rowcoord) <- afc$colnames
if (!col){
}
clnb <- ncol(chisqrtable)
- if (!col) classes <- as.matrix(apply(chitable,1,which.max))
- else classes <- 1:clnb
- ntabtot <- cbind(rowcoord, classes)
+ 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, 60)
+ rowcoord <- rowcoord[row.keep,]
+ classes <- classes[row.keep]
+ cex.par <- cex.par[row.keep]
+ } else {
+ classes <- 1:clnb
+ cex.par <- rep(1,clnb)
+ }
+ #ntabtot <- cbind(rowcoord, classes)
#if (!col) ntabtot <- ntabtot[row_keep,]
+ xlab <- paste('facteur ', x, ' -')
+ ylab <- paste('facteur ', y, ' -')
+ xlab <- paste(xlab,round(afc_table$facteur[x,2],2),sep = ' ')
+ xlab <- paste(xlab,' %%',sep = '')
+ ylab <- paste(ylab,round(afc_table$facteur[y,2],2),sep = ' ')
+ ylab <- paste(ylab,' %%',sep = '')
+
open_file_graph(filename, width = width, height = height)
par(cex=PARCEX)
- plot(rowcoord[,x],rowcoord[,y], pch='', xlab = xlab, ylab = ylab)
- abline(h=0,v=0)
- for (i in 1:clnb) {
- ntab <- subset(ntabtot,ntabtot[,ncol(ntabtot)] == i)
- if (nrow(ntab) != 0)
- text(ntab[,x],ntab[,y],rownames(ntab),col=rainbow(clnb)[i])
- }
- dev.off()
+
+ table.in <- rowcoord[order(cex.par, decreasing = TRUE),]
+ classes <- classes[order(cex.par, decreasing = TRUE)]
+ cex.par <- cex.par[order(cex.par, decreasing = TRUE)]
+ table.in <- stopoverlap(table.in, cex.par=cex.par)
+ classes <- classes[table.in[,4]]
+ cex.par <- cex.par[table.in[,4]]
+ make_afc_graph(table.in, classes, clnb, xlab, ylab, cex.txt = cex.par, xminmax=c(xmin,xmax), yminmax=c(ymin,ymax))
+
+ #plot(rowcoord[,x],rowcoord[,y], pch='', xlab = xlab, ylab = ylab)
+ #abline(h=0,v=0)
+ #for (i in 1:clnb) {
+ # ntab <- subset(ntabtot,ntabtot[,ncol(ntabtot)] == i)
+ # if (nrow(ntab) != 0)
+ # text(ntab[,x],ntab[,y],rownames(ntab),col=rainbow(clnb)[i])
+ #}
+ #dev.off()
}
filename.to.svg <- function(filename) {
open_file_graph <- function (filename, width=800, height = 800, quality = 100, svg = FALSE) {
if (Sys.info()["sysname"] == 'Darwin') {
- width <- width/74.97
- height <- height/74.97
- quartz(file = filename, type = 'jpeg', width = width, height = height)
+ width <- width/74.97
+ height <- height/74.97
+ if (!svg) {
+ quartz(file = filename, type = 'png', width = width, height = height)
+ } else {
+ svg(filename.to.svg(filename), width=width, height=height)
+ }
} else {
- #print('ATTENTION SVG!!!!!!!!!!!!!!!!!!!!!!!!!!!')
#library(RSvgDevice)
if (svg) {
svg(filename.to.svg(filename), width=width/74.97, height=height/74.97)
}
}
+#################################################@@
+#from wordcloud
+overlap <- function(x1, y1, sw1, sh1, boxes) {
+ use.r.layout <- FALSE
+ if(!use.r.layout)
+ return(.overlap(x1,y1,sw1,sh1,boxes))
+ s <- 0
+ if (length(boxes) == 0)
+ return(FALSE)
+ for (i in c(last,1:length(boxes))) {
+ bnds <- boxes[[i]]
+ x2 <- bnds[1]
+ y2 <- bnds[2]
+ sw2 <- bnds[3]
+ sh2 <- bnds[4]
+ if (x1 < x2)
+ overlap <- x1 + sw1 > x2-s
+ else
+ overlap <- x2 + sw2 > x1-s
+
+ if (y1 < y2)
+ overlap <- overlap && (y1 + sh1 > y2-s)
+ else
+ overlap <- overlap && (y2 + sh2 > y1-s)
+ if(overlap){
+ last <<- i
+ return(TRUE)
+ }
+ }
+ FALSE
+}
+
+.overlap <- function(x11,y11,sw11,sh11,boxes1){
+ .Call("is_overlap",x11,y11,sw11,sh11,boxes1)
+}
+########################################################
+stopoverlap <- function(x, cex.par = NULL) {
+#from wordcloud
+ library(wordcloud)
+ tails <- "g|j|p|q|y"
+ rot.per <- 0
+ last <- 1
+ thetaStep <- .1
+ rStep <- .5
+ toplot <- NULL
+
+# plot.new()
+ plot(x[,1],x[,2], pch='')
+
+ words <- rownames(x)
+ if (is.null(cex.par)) {
+ size <- rep(0.9, nrow(x))
+ } else {
+ size <- cex.par
+ }
+ #cols <- rainbow(clnb)
+ boxes <- list()
+ for (i in 1:nrow(x)) {
+ rotWord <- runif(1)<rot.per
+ r <-0
+ theta <- runif(1,0,2*pi)
+ x1<- x[i,1]
+ y1<- x[i,2]
+ wid <- strwidth(words[i],cex=size[i])
+ ht <- strheight(words[i],cex=size[i])
+ ht <- (ht + ht*.2) + .01
+ wid <- (wid + wid*.1) + .01
+ isOverlaped <- TRUE
+ while(isOverlaped){
+ if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht, boxes)) { #&&
+ toplot <- rbind(toplot, c(x1, y1, size[i], i))
+ #text(x1,y1,words[i],cex=size[i],offset=0,srt=rotWord*90,
+ # col=cols[classes[i]])
+ boxes[[length(boxes)+1]] <- c(x1-.5*wid,y1-.5*ht,wid,ht)
+ isOverlaped <- FALSE
+ } else {
+ if(r>sqrt(.5)){
+ print(paste(words[i], "could not be fit on page. It will not be plotted."))
+ isOverlaped <- FALSE
+ }
+ theta <- theta+thetaStep
+ r <- r + rStep*thetaStep/(2*pi)
+ x1 <- x[i,1]+r*cos(theta)
+ y1 <- x[i,2]+r*sin(theta)
+ }
+ }
+ }
+ row.names(toplot) <- words[toplot[,4]]
+ return(toplot)
+}
+###############################################################################
+
make_tree_tot <- function (chd) {
library(ape)
lf<-chd$list_fille
dendro <- gsub('a','',dendro)
dendro_tot_cl <- read.tree(text = dendro)
#FIXME
- for (i in 1:10) {
+ for (i in 1:100) {
for (cl in 1:clnb) {
dendro <- gsub(paste('\\(',cl,',',cl,'\\)',sep=''),cl,dendro)
}
}
- for (i in 1:10) {
+ for (i in 1:100) {
dendro <- gsub(paste('\\(',0,',',0,'\\)',sep=''),0,dendro)
for (cl in 1:clnb) {
dendro <- gsub(paste('\\(',0,',',cl,'\\)',sep=''),cl,dendro)
row_keep
}
+select.chi.classe <- function(tablechi, nb) {
+ rowkeep <- NULL
+ if (nb > nrow(tablechi)) {
+ nb <- nrow(tablechi)
+ }
+ for (i in 1:ncol(tablechi)) {
+ rowkeep <- append(rowkeep,order(tablechi[,i], decreasing = TRUE)[1:nb])
+ }
+ rowkeep <- unique(rowkeep)
+ rowkeep
+}
+
#from summary.ca
summary.ca.dm <- function(object, scree = TRUE, ...){
obj <- object
res
}
-make_afc_graph <- function(toplot,classes,clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE) {
+make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) {
+ if (is.null(xminmax)) {
+ xminmax <- c(min(toplot[,1], na.rm = TRUE) + (0.1 * min(toplot[,1], na.rm = TRUE)), max(toplot[,1], na.rm = TRUE) + (0.1 * max(toplot[,1], na.rm = TRUE)))
+ }
+ if (is.null(yminmax)) {
+ yminmax <- c(min(toplot[,2], na.rm = TRUE) + (0.1 * min(toplot[,2], na.rm = TRUE)), max(toplot[,2], na.rm = TRUE) + (0.1 * max(toplot[,2], na.rm = TRUE)))
+ }
rain <- rainbow(clnb)
compt <- 1
tochange <- NULL
}
}
cl.color <- rain[classes]
- plot(toplot[,1],toplot[,2], pch='', xlab = xlab, ylab = ylab)
- abline(h=0,v=0, lty = 'dashed')
+ if (black) {
+ cl.color <- 'black'
+ }
+ 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))
- text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color)
+ text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, offset=0)
else
- text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, cex = cex.txt)
+ text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, cex = cex.txt, offset=0)
if (!cmd) {
dev.off()
cc<-mc[cc]
#mass<-(rowSums(x)/max(rowSums(x))) * 5
maxchi<-norm.vec(maxchi, 0.03, 0.3)
- rglplot(g1,vertex.label = vire.nonascii(rownames(x)),vertex.label.color='black',vertex.color=cc,vertex.size = 0.1, layout=lo, rescale=FALSE)
- rgl.spheres(lo, col = cc, radius = maxchi, alpha = alpha)
+ rglplot(g1,vertex.label = vire.nonascii(rownames(x)),vertex.label.color= cc,vertex.label.cex = maxchi, vertex.size = 0.1, layout=lo, rescale=FALSE)
+ text3d(lo[,1], lo[,2],lo[,3], rownames(x), cex=maxchi, col=cc)
+ #rgl.spheres(lo, col = cc, radius = maxchi, alpha = alpha)
rgl.bg(color = c('white','black'))
if (!is.null(movie)) {
require(tcltk)
projects / iramuteq / blobdiff