From 95e2cecec9e4eb2d1e5a0fed0b08690337f9d4b9 Mon Sep 17 00:00:00 2001 From: Pierre Ratinaud Date: Mon, 7 May 2018 10:46:40 +0200 Subject: [PATCH] correction for ape 5.1 --- Rscripts/Rgraph.R | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R index 12938bf..e758cfb 100644 --- a/Rscripts/Rgraph.R +++ b/Rscripts/Rgraph.R @@ -680,12 +680,12 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro colcloud <- rainbow(length(sum.cl)) colcloud <- del.yellow(colcloud) } - label.ori<-tree[[2]] + label.ori<-tree$tip.label if (!is.null(lab)) { tree$tip.label <- lab } else { - tree[[2]]<-paste('classe ',tree[[2]]) - } + tree$tip.label<-paste('classe ',tree$tip.label) + } 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 = 1.5, y.lim=c(-0.3,tree$Nnode)) par(mar=c(0,0,0,0)) @@ -748,12 +748,12 @@ plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendr colcloud <- rainbow(length(sum.cl)) } par(mar=c(0,0,0,0)) - label.ori<-tree[[2]] + label.ori<-tree$tip.label if (!is.null(lab)) { tree$tip.label <- lab } else { - tree[[2]]<-paste('classe ',tree[[2]]) - } + tree$tip.label<-paste('classe ',tree$tip.label) + } plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro) for (i in rev(tree.order)) { par(mar=c(0,0,1,0),cex=0.9) @@ -862,11 +862,11 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2 } layout(matlay, widths=lay.width,TRUE) par(mar=c(3,0,2,4),cex=1) - label.ori<-tree[[2]] + label.ori<-tree$tip.label if (!is.null(lab)) { - tree$tip.label <- lab[tree.order] + tree$tip.label <- lab } else { - tree[[2]]<-paste('classe ',tree[[2]]) + tree$tip.label<-paste('classe ',tree$tip.label) } to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot))) if (!bw) { -- 2.7.4