[Adephylo-commits] r127 - in pkg: R man

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2009-11-05 12:08:02 +0100 (Thu, 05 Nov 2009)
New Revision: 127

Modified:
   pkg/R/table.phylo4d.R
   pkg/man/lizards.Rd
   pkg/man/table.phylo4d.Rd
Log:
again tip.label issues.


Modified: pkg/R/table.phylo4d.R
===================================================================
--- pkg/R/table.phylo4d.R	2009-11-05 11:05:15 UTC (rev 126)
+++ pkg/R/table.phylo4d.R	2009-11-05 11:08:02 UTC (rev 127)
@@ -86,7 +86,7 @@
     y.inset <- SYMBSCALE * cex.symbol * usr.height / par("pin")[2]
     x.base <- plotres$x.lim[2] + x.inset # start plotting from x.base rightwards
     if(show.tip.label){
-        temp <- x at tip.label[which.max(nchar(tipLabels(x)))] # longest tip label
+        temp <- tipLabels(x)[which.max(nchar(tipLabels(x)))] # longest tip label
         lab.width <- strwidth(temp, units="user", cex=cex.label) # compute the width to keep for tip labels
     } else{
         lab.width <- 0

Modified: pkg/man/lizards.Rd
===================================================================
--- pkg/man/lizards.Rd	2009-11-05 11:05:15 UTC (rev 126)
+++ pkg/man/lizards.Rd	2009-11-05 11:08:02 UTC (rev 127)
@@ -51,7 +51,7 @@
 ## remove size effect
 temp <- lapply(liz.pca1$tab, function(e) residuals(lm(e~-1+liz.pca1$li[,1])) )
 temp <- data.frame(temp)
-row.names(temp) <- liz at tip.label
+row.names(temp) <- tipLabels(liz)
 
 ## build corresponding phylo4d object
 liz.noSize <- phylo4d(liz.tr, temp)

Modified: pkg/man/table.phylo4d.Rd
===================================================================
--- pkg/man/table.phylo4d.Rd	2009-11-05 11:05:15 UTC (rev 126)
+++ pkg/man/table.phylo4d.Rd	2009-11-05 11:08:02 UTC (rev 127)
@@ -18,7 +18,7 @@
                       repVar=1:ncol(tdata(x, type="tip")), center=TRUE, scale=TRUE, legend=TRUE, grid=TRUE, box=TRUE,
                       show.tip.label=TRUE, show.node.label=TRUE, show.var.label=TRUE,
                       ratio.tree=1/3, font=3,
-                      tip.label=x at tip.label, var.label=colnames(tdata(x,type="tip")),
+                      tip.label=tipLabels(x), var.label=colnames(tdata(x,type="tip")),
                       cex.symbol=1, cex.label=1, cex.legend=1,
   coord.legend=NULL, \dots)
 }