From dbd43dfa2a70c764332cf4694e22f29ca14b3539 Mon Sep 17 00:00:00 2001 From: Pierre Ratinaud Date: Tue, 30 May 2017 11:25:26 +0200 Subject: [PATCH] labels order in dendro + bar graphics --- Rscripts/Rgraph.R | 60 +++++++++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 54 insertions(+), 6 deletions(-) diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R index 4a23d3e..dacd7a8 100644 --- a/Rscripts/Rgraph.R +++ b/Rscripts/Rgraph.R @@ -107,7 +107,7 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto 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$toplot + table.in <- table.out$toplot notplot <- table.out$notplot if (! is.null(notplot)) { write.csv2(notplot, file = paste(filename, '_notplotted.csv', sep = '')) @@ -226,7 +226,7 @@ stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) { isOverlaped <- FALSE } else { if(r>sqrt(.5)){ - print(paste(words[i], "could not be fit on page. It will not be plotted.")) + #print(paste(words[i], "could not be fit on page. It will not be plotted.")) notplot <- rbind(notplot,c(words[i], x[i,1], x[i,2], size[i], i)) isOverlaped <- FALSE } @@ -237,6 +237,8 @@ stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) { } } } + nbnot <- nrow(notplot) + print(paste(nbnot, ' not plotted')) row.names(toplot) <- words[toplot[,4]] return(list(toplot = toplot, notplot = notplot)) } @@ -343,6 +345,19 @@ getwordcloudcoord <- function(words,freq,scale=c(4,.5),min.freq=3,max.words=Inf, return(toplot) } +new_tree_tot <- function(chd) { + lf <- chd$list_fille + m <- matrix(0, ncol=2) + for (val in 1:length(lf)) { + if (! is.null(lf[[val]])) { + print(c(val,lf[[val]][1])) + m <- rbind(m, c(val,lf[[val]][1])) + m <- rbind(m, c(val,lf[[val]][2])) + } + } + m[-1,] +} + make_tree_tot <- function (chd) { library(ape) lf<-chd$list_fille @@ -582,7 +597,7 @@ del.yellow <- function(colors) { colors } -make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) { +make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL, color=NULL) { rain <- rainbow(clnb) compt <- 1 @@ -607,6 +622,9 @@ make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, le if (black) { cl.color <- 'black' } + if (!is.null(color)) { + cl.color <- color + } plot(toplot[,1],toplot[,2], pch='', xlab = xlab, ylab = ylab, xlim=xminmax, ylim = yminmax) abline(h=0, v=0, lty = 'dashed') if (is.null(cex.txt)) @@ -669,7 +687,7 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro tree[[2]]<-paste('classe ',tree[[2]]) } par(mar=c(2,1,0,1)) - plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1, y.lim=c(-0.3,tree$Nnode)) + plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.5, y.lim=c(-0.3,tree$Nnode)) par(mar=c(0,0,0,0)) d <- barplot(-sum.cl[tree.order], col=col, names.arg='', axes=FALSE, axisname=FALSE) text(x=d, y=(-sum.cl[tree.order]+3), label=paste(round(sum.cl[tree.order],1),'%'), cex=1) @@ -678,7 +696,7 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro #wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(1.5, 0.2), random.order=FALSE, colors = colcloud[i]) yval <- 1.1 plot(0,0,pch='', axes = FALSE) - vcex <- norm.vec(lclasses[[i]], 1, 3) + vcex <- norm.vec(lclasses[[i]], 2, 3) for (j in 1:length(lclasses[[i]])) { yval <- yval-(strheight( names(lclasses[[i]])[j],cex=vcex[j])+0.02) text(-0.9, yval, names(lclasses[[i]])[j], cex = vcex[j], col = colcloud[i], adj=0) @@ -900,7 +918,7 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2 } par(mar=c(0,0,0,0)) plot(0, axes = FALSE, pch = '') - legend(x = 'center' , rownames(to.plot), fill = col.bars) + legend(x = 'center' , rev(rownames(to.plot)), fill = rev(col.bars)) if (!cmd) { dev.off() } @@ -1136,6 +1154,7 @@ graphml.to.file <- function(graph.path) { } + graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) { require(igraph) g <- graph.simi$graph @@ -1179,3 +1198,32 @@ graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, commun df } } + +graph.to.file2 <- function(graph, layout, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) { + require(igraph) + g <- graph + V(g)$x <- layout[,1] + V(g)$y <- layout[,2] + if (ncol(layout) == 3) { + V(g)$z <- layout[,3] + } + v.colors <- col2rgb(V(g)$color) + V(g)$r <- v.colors[1,] + V(g)$g <- v.colors[2,] + V(g)$b <- v.colors[3,] + + if (!is.null(sweight)) { + V(g)$sweight <- sweight + } + df <- get.data.frame(g, what='both') + if (!is.null(nodesfile)) { + write.table(df$vertices, nodesfile, sep='\t', row.names=FALSE) + } + if (!is.null(edgesfile)) { + write.table(df$edges, edgesfile, sep='\t', row.names=FALSE) + } + if (is.null(edgesfile) & is.null(nodesfile)) { + df + } +} + -- 2.7.4