save(tree.cut1, file="%s")
classes<-n1[,ncol(n1)]
open_file_graph("%s", width = 600, height=400)
- plot.dendropr(tree.cut1$tree.cl,classes)
+ plot.dendropr(tree.cut1$tree.cl,classes, histo=TRUE)
open_file_graph("%s", width = 600, height=400)
plot(tree.cut1$dendro_tot_cl)
dev.off()
""" % (DictChdTxtOut['afc_facteur'], DictChdTxtOut['afc_col'], DictChdTxtOut['afc_row'])
txt += """
- xlab <- paste('facteur 1 - ', round(afc$facteur[1,2],2), sep = '')
- ylab <- paste('facteur 2 - ', round(afc$facteur[2,2],2), sep = '')
- xlab <- paste(xlab, ' %', sep = '')
- ylab <- paste(ylab, ' %', sep = '')
+ #xlab <- paste('facteur 1 - ', round(afc$facteur[1,2],2), sep = '')
+ #ylab <- paste('facteur 2 - ', round(afc$facteur[2,2],2), sep = '')
+ #xlab <- paste(xlab, ' %', sep = '')
+ #ylab <- paste(ylab, ' %', sep = '')
"""
txt += """
PARCEX<-%s
+ xmin <- min(afc$rowcoord[,1]) + (0.1 * min(afc$rowcoord[,1]))
+ xmax <- max(afc$rowcoord[,1]) + (0.1 * max(afc$rowcoord[,1]))
+ ymin <- min(afc$rowcoord[,2]) + (0.1 * min(afc$rowcoord[,2]))
+ ymax <- max(afc$rowcoord[,2]) + (0.1 * max(afc$rowcoord[,2]))
""" % taillecar
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
""" % (DictChdTxtOut['AFC2DL_OUT'])
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
""" % (DictChdTxtOut['AFC2DSL_OUT'])
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
""" % (DictChdTxtOut['AFC2DEL_OUT'])
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab)
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
""" % (DictChdTxtOut['AFC2DCL_OUT'])
- txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='crl', xlab = xlab, ylab = ylab)
- """ % (DictChdTxtOut['AFC2DCoul'], DictChdTxtOut['AFC2DCoulSup'], DictChdTxtOut['AFC2DCoulEt'], DictChdTxtOut['AFC2DCoulCl'])
+# txt += """
+ # PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
+ # PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
+ # PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
+ # PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='crl', xlab = xlab, ylab = ylab)
+ # """ % (DictChdTxtOut['AFC2DCoul'], DictChdTxtOut['AFC2DCoulSup'], DictChdTxtOut['AFC2DCoulEt'], DictChdTxtOut['AFC2DCoulCl'])
txt += """
#rm(dataact)
############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
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])
}
res
}
-make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = 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]) + (0.1 * min(toplot[,1])), max(toplot[,1]) + (0.1 * max(toplot[,1])))
+ }
+ if (is.null(yminmax)) {
+ yminmax <- c(min(toplot[,2]) + (0.1 * min(toplot[,2])), max(toplot[,2]) + (0.1 * max(toplot[,2])))
+ }
rain <- rainbow(clnb)
compt <- 1
tochange <- NULL
if (black) {
cl.color <- 'black'
}
- plot(toplot[,1],toplot[,2], pch='', xlab = xlab, ylab = ylab)
+ 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, offset=0)
}
}
-#################################################@@
-#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])
- if(grepl(tails,words[i]))
- ht <- ht + ht*.2
- if(rotWord){
- tmp <- ht
- ht <- wid
- wid <- tmp
- }
- 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)
-}
-###############################################################################
if (typegraph == 0) {
parcex <- taillecar/10
par(cex = parcex)
if (over) {
+ table.in <- table.in[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]]
projects / iramuteq / commitdiff