[adegenet-commits] r1049 - pkg/R

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

Author: jombart
Date: 2012-11-08 17:44:10 +0100 (Thu, 08 Nov 2012)
New Revision: 1049

Modified:
   pkg/R/sequences.R
Log:
started a (commented) graphic version of findMutations

Modified: pkg/R/sequences.R
===================================================================
--- pkg/R/sequences.R	2012-11-08 14:13:56 UTC (rev 1048)
+++ pkg/R/sequences.R	2012-11-08 16:44:10 UTC (rev 1049)
@@ -206,11 +206,33 @@
 
 
 
+## ##################
+## ## graphMutations
+## ##################
+## graphMutations <- function(x, plot=TRUE, ...){
+##     if(!require(igraph)) stop("igraph is required")
 
+##     ## GET GRAPH ##
+##     from.old <- gsub("->.*","",names(x))
+##     to.old <- gsub(".*->","",names(x))
+##     vnames <- sort(unique(c(from.old,to.old)))
+##     from <- match(from.old,vnames)
+##     to <- match(to.old,vnames)
+##     dat <- data.frame(from,to,stringsAsFactors=FALSE)
+##     out <- graph.data.frame(dat, directed=TRUE)
 
+##     ## SET VERTICES LABELS ##
+##     V(out)$label <- vnames
 
+##     ## SET ANNOTATIONS FOR THE BRANCHES ##
+##     annot <- unlist(lapply(x, function(e) paste(e$short, collapse="\n")))
+##     E(out)$label <- annot
 
+##     ## PLOT / RETURN ##
+##     if(plot) plot(out, ...)
 
+##     return(out)
+## } # end graphMutations
 
 
 
@@ -220,6 +242,11 @@
 
 
 
+
+
+
+
+
 ## ###############
 ## ## transiProb
 ## ###############