X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=Rscripts%2FRgraph.R;h=e947a402ed0e5993681e790cac77a8ed0215a1f3;hp=1caf440ccd050f0cc55d2bc7a21247e5ad400833;hb=2ffa9388c45dce689bb45c1cf6c7ad81d2636409;hpb=13666be5de5eeffbe63774c3c0aecd407b519ac6 diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R index 1caf440..e947a40 100644 --- a/Rscripts/Rgraph.R +++ b/Rscripts/Rgraph.R @@ -1,18 +1,18 @@ ############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) @@ -30,20 +30,20 @@ PlotDendroCut <- function(chd,filename,reso,clusternb) { 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=NULL) { if (col) { if (what == 'coord') { rowcoord <- as.matrix(afc$colcoord) @@ -59,7 +59,6 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto } x <- axetoplot[1] y <- axetoplot[2] - if (col) rownames(rowcoord) <- afc$colnames if (!col){ @@ -73,20 +72,59 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto } 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, 80) + rowcoord <- rowcoord[row.keep,] + classes <- classes[row.keep] + cex.par <- cex.par[row.keep] + } else { + classes <- 1:clnb + cex.par <- rep(1,clnb) + } + if (is.null(xmin)) { + table.in <- rowcoord + xminmax <- c(min(table.in[,1], na.rm = TRUE) + ((max(cex.par)/10) * min(table.in[,1], na.rm = TRUE)), max(table.in[,1], na.rm = TRUE) + ((max(cex.par)/10) * max(table.in[,1], na.rm = TRUE))) + xmin <- xminmax[1] + xmax <- xminmax[2] + yminmax <- c(min(table.in[,2], na.rm = TRUE) + ((max(cex.par)/10) * min(table.in[,2], na.rm = TRUE)), max(table.in[,2], na.rm = TRUE) + ((max(cex.par)/10) * max(table.in[,2], na.rm = TRUE))) + ymin <- yminmax[1] + ymax <- yminmax[2] + } + #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.out <- stopoverlap(table.in, cex.par=cex.par, xlim = c(xmin,xmax), ylim = c(ymin,ymax)) + table.in <- table.out$toplot + notplot <- table.out$notplot + if (! is.null(notplot)) { + write.csv2(notplot, file = paste(filename, '_notplotted.csv', sep = '')) + } + 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)) + xyminmax <- list(yminmax = c(ymin,ymax), xminmax = c(xmin,xmax)) + xyminmax + #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) { @@ -96,11 +134,14 @@ 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) @@ -110,6 +151,98 @@ open_file_graph <- function (filename, width=800, height = 800, quality = 100, s } } +#################################################@@ +#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, xlim = NULL, ylim = NULL) { +#from wordcloud + library(wordcloud) + tails <- "g|j|p|q|y" + rot.per <- 0 + last <- 1 + thetaStep <- .1 + rStep <- .5 + toplot <- NULL + notplot <- NULL + +# plot.new() + plot(x[,1],x[,2], pch='', xlim = xlim, ylim = ylim) + + 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)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])) + 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(list(toplot = toplot, notplot = notplot)) +} +############################################################################### + make_tree_tot <- function (chd) { library(ape) lf<-chd$list_fille @@ -146,12 +279,12 @@ make_dendro_cut_tuple <- function(dendro_in, coordok, classeuce, x, nbt = 9) { 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) @@ -185,6 +318,9 @@ select_point_chi <- function(tablechi, chi_limit) { 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]) } @@ -305,8 +441,9 @@ create_afc_table <- function(x) { res } -make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE) { - rain <- rainbow(clnb) +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) compt <- 1 tochange <- NULL for (my.color in rain) { @@ -328,7 +465,7 @@ make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, le 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) @@ -340,16 +477,120 @@ make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, le } } +plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro = "phylogram", from.cmd = FALSE, bw = FALSE, lab = NULL) { + library(ape) + library(wordcloud) + 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])) + sum.cl <- sum.cl[,1] + tree.order<- as.numeric(tree$tip.label) + vec.mat<-NULL + row.keep <- select.chi.classe(chisqtable, nbbycl) + toplot <- chisqtable[row.keep,] + lclasses <- list() + for (classe in 1:length(sum.cl)) { + ntoplot <- toplot[,classe] + ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)] + ntoplot <- round(ntoplot, 0) + ntoplot <- ntoplot[1:nbbycl] + #ntoplot <- ntoplot[order(ntoplot)] + #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)) + if (! bw) { + col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)] + colcloud <- rainbow(length(sum.cl)) + } + par(mar=c(1,0,0,0)) + label.ori<-tree[[2]] + if (!is.null(lab)) { + tree$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) + 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) + 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) + } + } + +} + +plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro = "phylogram", from.cmd = FALSE, bw = FALSE, lab = NULL) { + library(wordcloud) + library(ape) + 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])) + sum.cl <- sum.cl[,1] + tree.order<- as.numeric(tree$tip.label) + vec.mat<-NULL + row.keep <- select.chi.classe(chisqtable, nbbycl) + toplot <- chisqtable[row.keep,] + lclasses <- list() + for (classe in 1:length(sum.cl)) { + ntoplot <- toplot[,classe] + ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)] + ntoplot <- round(ntoplot, 0) + ntoplot <- ntoplot[1:nbbycl] + ntoplot <- ntoplot[order(ntoplot)] + #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot) + lclasses[[classe]] <- ntoplot + } + for (i in 1:length(sum.cl)) vec.mat<-append(vec.mat,1) + v<-2 + for (i in 1:length(sum.cl)) { + vec.mat<-append(vec.mat,v) + v<-v+1 + } + layout(matrix(vec.mat,length(sum.cl),2),widths=c(1,2)) + if (! bw) { + col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)] + colcloud <- rainbow(length(sum.cl)) + } + par(mar=c(0,0,0,0)) + label.ori<-tree[[2]] + if (!is.null(lab)) { + tree$tip.label <- lab + } else { + tree[[2]]<-paste('classe ',tree[[2]]) + } + plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro) + for (i in rev(tree.order)) { + par(mar=c(0,0,1,0),cex=0.9) + wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(4, 0.8), random.order=FALSE, colors = colcloud[i]) + } +} + plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, from.cmd=FALSE, bw=FALSE, lab = NULL, tclasse=TRUE) { classes<-classes[classes!=0] classes<-as.factor(classes) - sum.cl<-as.matrix(summary(classes)) + sum.cl<-as.matrix(summary(classes, maxsum=1000000)) sum.cl<-(sum.cl/colSums(sum.cl)*100) sum.cl<-round(sum.cl,2) sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1])) tree.order<- as.numeric(tree$tip.label) + + if (! bw) { - col = rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)] + col <- rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)] col.bars <- col col.pie <- rainbow(nrow(sum.cl)) #col.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])]