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correction for ape 5.1
author
Pierre Ratinaud
<ratinaud@univ-tlse2.fr>
Mon, 7 May 2018 08:46:40 +0000
(10:46 +0200)
committer
Pierre Ratinaud
<ratinaud@univ-tlse2.fr>
Mon, 7 May 2018 08:46:40 +0000
(10:46 +0200)
Rscripts/Rgraph.R
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diff --git
a/Rscripts/Rgraph.R
b/Rscripts/Rgraph.R
index
12938bf
..
e758cfb
100644
(file)
--- 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)
}
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 {
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$Nnode))
par(mar=c(0,0,0,0))
par(mar=c(2,1,0,1))
plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.5, y.lim=c(-0.3,tree$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))
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 {
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)
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)
}
layout(matlay, widths=lay.width,TRUE)
par(mar=c(3,0,2,4),cex=1)
- label.ori<-tree
[[2]]
+ label.ori<-tree
$tip.label
if (!is.null(lab)) {
if (!is.null(lab)) {
- tree$tip.label <- lab
[tree.order]
+ tree$tip.label <- lab
} else {
} 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) {
}
to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot)))
if (!bw) {