[adegenet-commits] r415 - pkg/R

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

Author: jombart
Date: 2009-06-19 22:17:03 +0200 (Fri, 19 Jun 2009)
New Revision: 415

Modified:
   pkg/R/seqTrack.R
Log:
Fixed major bug in color handling in plotSeqTrack: color was not subsetted for the NAs, and was recycled at the wrong time.
Is now ok.


Modified: pkg/R/seqTrack.R
===================================================================
--- pkg/R/seqTrack.R	2009-06-19 00:13:48 UTC (rev 414)
+++ pkg/R/seqTrack.R	2009-06-19 20:17:03 UTC (rev 415)
@@ -139,7 +139,7 @@
 ################
 plotSeqTrack <- function(x, xy, useArrows=TRUE, annot=TRUE, dateRange=NULL,
                          col=NULL, bg="grey", add=FALSE, quiet=FALSE,
-                         showAmbiguous=TRUE, mu0=NULL, chr.length=NULL, prob=0.75,
+                         showAmbiguous=FALSE, mu0=NULL, chr.length=NULL, prob=0.75,
                          plot=TRUE,...){
 
     ## CHECKS ##
@@ -153,12 +153,20 @@
 
     isAmbig <- NULL
 
+    ## RECYCLE COL
+    if(!is.null(col)){
+        col <- rep(col,length=nrow(x))
+    }
 
+
     ## SUBSET DATA (REMOVE NAs) ##
     isNA <- is.na(x[,2])
     x <- x[!isNA,,drop=FALSE]
     xy.all <- xy ## used to retrieve all coordinates
     xy <- xy[!isNA,,drop=FALSE]
+    if(!is.null(col)){
+        col <- col[!isNA]
+    }
 
 
     ## FIND AMBIGUOUS TEMPORAL ORDERING ##
@@ -181,7 +189,7 @@
     ## FIND THE COLOR FOR EDGES ##
     if(is.null(col)){
         if(is.null(mu0) & is.null(chr.length)) {
-            col <- "black"
+            col <- rep("black", length(x.from))
         } else {
             ##  w <- .pAbeforeB(x$ances.date, x$date, mu0, chr.length, 200) # beware, lots of steps take time
             ##             isAmbig <-  w < prob
@@ -216,10 +224,6 @@
     ##     }
 
 
-    ## recycle col
-    col <- rep(col,length=length(x.from))
-
-
     ## HANDLE RANGE OF DATES ##
     if(!is.null(dateRange)){