From 4f2dc8e6823ac5886f758a6ad3f1ae6acb01916c Mon Sep 17 00:00:00 2001 From: Pierre Date: Tue, 11 Feb 2014 14:06:32 +0100 Subject: [PATCH] new graphics : not ready :) --- Rscripts/CHD.R | 2 +- Rscripts/Rgraph.R | 184 ++++++++++++++++++++++++++++++++++++++++++++++----- Rscripts/afc_graph.R | 10 ++- Rscripts/chdfunct.R | 4 +- Rscripts/chdtxt.R | 2 +- 5 files changed, 177 insertions(+), 25 deletions(-) diff --git a/Rscripts/CHD.R b/Rscripts/CHD.R index 974e901..e6a3c7b 100644 --- a/Rscripts/CHD.R +++ b/Rscripts/CHD.R @@ -1,6 +1,6 @@ #Author: Pierre Ratinaud #Copyright (c) 2008-2011 Pierre Ratinaud -#Lisense: GNU/GPL +#License: GNU/GPL pp<-function(txt,val) { d<-paste(txt,' : ') diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R index e947a40..da03d5b 100644 --- a/Rscripts/Rgraph.R +++ b/Rscripts/Rgraph.R @@ -43,7 +43,7 @@ PlotDendroCut <- function(chd,filename,reso,clusternb) { # 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) @@ -75,7 +75,7 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto 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] @@ -142,7 +142,6 @@ open_file_graph <- function (filename, width=800, height = 800, quality = 100, s 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 { @@ -316,8 +315,13 @@ select_point_chi <- function(tablechi, chi_limit) { 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) } @@ -441,6 +445,29 @@ create_afc_table <- function(x) { 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) @@ -494,6 +521,7 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro 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] @@ -501,27 +529,33 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro #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) @@ -591,8 +625,10 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f if (! bw) { col <- rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)] + col <- del.yellow(col) col.bars <- col col.pie <- rainbow(nrow(sum.cl)) + col.pie <- del.yellow(col.pie) #col.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])] } else { col = 'black' @@ -644,10 +680,24 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f } #tree <- tree.cut1$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$tip.label) + if (!is.null(classes)) { + classes<-classes[classes!=0] + classes<-as.factor(classes) + sum.cl<-as.matrix(summary(classes, maxsum=1000000)) + sum.cl<-(sum.cl/colSums(sum.cl)*100) + sum.cl<-round(sum.cl,2) + sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1])) + } par(mar=c(0,0,0,0)) - layout(matrix(c(1,2,3),1,byrow=TRUE), widths=lay.width,TRUE) + if (!is.null(classes)) { + matlay <- matrix(c(1,2,3,4),1,byrow=TRUE) + lay.width <- c(3,1,3,2) + } else { + matlay <- matrix(c(1,2,3),1,byrow=TRUE) + } + layout(matlay, widths=lay.width,TRUE) par(mar=c(3,0,2,0),cex=1) label.ori<-tree[[2]] if (!is.null(lab)) { @@ -657,15 +707,27 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2 } to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot))) if (!bw) { - col <- rainbow(ncol(to.plot)) - col.bars <- rainbow(nrow(to.plot)) + col <- rainbow(ncol(to.plot)) + col <- del.yellow(col) + if (is.null(colbar)) { + col.bars <- rainbow(nrow(to.plot)) + col.bars <- del.yellow(col.bars) + } else { + col.bars <- colbar + } } else { col <- 'black' col.bars <- grey.colors(nrow(to.plot),0,0.8) } col <- col[tree.order] plot.phylo(tree,label.offset=0.1,tip.col=col) - + if (!is.null(classes)) { + par(cex=0.7) + par(mar=c(3,0,2,1)) + to.plota <- sum.cl[tree.order,1] + d <- barplot(to.plota,horiz=TRUE, col=col, names.arg='', axes=FALSE, axisname=FALSE) + text(x=to.plota, y=d[,1], label=paste(round(to.plota,1),'%'), adj=1.2) + } par(mar=c(3,0,2,1)) d <- barplot(to.plot,horiz=TRUE, col=col.bars, beside=TRUE, names.arg='', space = c(0.1,0.6), axisname=FALSE) c <- colMeans(d) @@ -827,3 +889,95 @@ vire.nonascii <- function(rnames) { #d <- barplot(to.plot,horiz=TRUE, names.arg='', axes=FALSE, axisname=FALSE) #text(x=to.plot, y=d[,1], label=round(to.plot,1), adj=1.2) +make.afc.attributes <- function(rn, afc.table, contafc, clnb, column = FALSE, x=1, y=2) { + if (!column){ + nd <- clnb - 1 + afc.res <- afc.table$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)$name)) + colnames(nodes) <- c('id', 'label') + print(nodes) + if (! is.null(nodes.attr)) { + nodesatt <- as.data.frame(nodes.attr) + } else { + nodesatt <- data.frame(cbind(lo[,1],lo[,2])) + } + edges <- as.data.frame(get.edges(g, c(1:ecount(g)))) + col <- rep('red', nrow(lo)) + col <- t(sapply(col, col2rgb, alpha=TRUE)) + write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo)) +} diff --git a/Rscripts/afc_graph.R b/Rscripts/afc_graph.R index 918211e..bda5ce7 100644 --- a/Rscripts/afc_graph.R +++ b/Rscripts/afc_graph.R @@ -1,6 +1,6 @@ #Author: Pierre Ratinaud #Copyright (c) 20010-2013 Pierre Ratinaud -#Lisense: GNU/GPL +#License: GNU/GPL #fichier genere par IRaMuTeq @@ -130,7 +130,7 @@ if ( qui == 3 ) { table.in <- table.in[row.keep,] tablechi <- tablechi[row.keep,] } else if (do.select.chi.classe) { - row.keep <- select.chi.classe(tablechi, ptbycluster) + row.keep <- select.chi.classe(tablechi, ptbycluster, active=FALSE) table.in <- table.in[row.keep,] tablechi <- tablechi[row.keep,] } else { @@ -195,9 +195,7 @@ if (typegraph == 0 || typegraph == 2) { if (qui != 3) { tokeep <- rownames(chistabletot) %%in%% rownames(table.in) chis <- chistabletot[tokeep,] - if (over) { - chis<-chis[rownames(table.in),] - } + chis<-chis[rownames(table.in),] nodes.attr$chiclasse <- chis } else { chis <- NULL @@ -249,7 +247,7 @@ if (typegraph == 0 || typegraph == 2) { ReturnVal <- tkmessageBox(title="RGL 3 D",message="Fini !",icon="info",type="ok") } - if (typegraph == 2) { + if (typegraph == 1) { require(tcltk) ReturnVal <- tkmessageBox(title="RGL 3 D",message="Cliquez pour fermer",icon="info",type="ok") } else { diff --git a/Rscripts/chdfunct.R b/Rscripts/chdfunct.R index a2dc502..5e31442 100644 --- a/Rscripts/chdfunct.R +++ b/Rscripts/chdfunct.R @@ -294,8 +294,8 @@ AsLexico2<- function(mat, chip = FALSE) { } make.spec.hypergeo <- function(mat) { - library(textometrieR) - spec <- specificites(mat) + library(textometry) + spec <- specificities(mat) sumcol<-colSums(mat) eff_relatif<-round(t(apply(mat,1,function(x) {(x/t(as.matrix(sumcol))*1000)})),2) colnames(eff_relatif) <- colnames(mat) diff --git a/Rscripts/chdtxt.R b/Rscripts/chdtxt.R index 13077f0..8d0c290 100644 --- a/Rscripts/chdtxt.R +++ b/Rscripts/chdtxt.R @@ -1,6 +1,6 @@ #Author: Pierre Ratinaud #Copyright (c) 2008-2009 Pierre Ratinaud -#Lisense: GNU/GPL +#License: GNU/GPL #fonction pour la double classification -- 2.7.4