[adegenet-commits] r422 - pkg/R

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

Author: jombart
Date: 2009-06-23 14:17:06 +0200 (Tue, 23 Jun 2009)
New Revision: 422

Modified:
   pkg/R/haploSim.R
   pkg/R/seqTrack.R
Log:
various fixes to make both files compatible.


Modified: pkg/R/haploSim.R
===================================================================
--- pkg/R/haploSim.R	2009-06-23 11:51:01 UTC (rev 421)
+++ pkg/R/haploSim.R	2009-06-23 12:17:06 UTC (rev 422)
@@ -476,7 +476,7 @@
 
     ## CALL TO PLOTSEQTRACK ##
     plotSeqTrack(x=res, xy=xy, annot=annot, dateRange=dateRange,
-                        col=col, bg=bg, add=add, showAmbiguous=FALSE, ...)
+                        col=col, bg=bg, add=add, ...)
 
     return(invisible(res))
 
@@ -516,7 +516,7 @@
         sampdates <- .rTimeSeq(mu0=mu0, L=L, n=length(truedates), maxNbDays=daterange/2)
     } else{
         arg.rDate$n <- n
-        sampdates <- do.call(.rTimeSeq, arg.rDate)
+        sampdates <- do.call(rDate, arg.rDate)
     }
     sampdates <- truedates + abs(sampdates)
 

Modified: pkg/R/seqTrack.R
===================================================================
--- pkg/R/seqTrack.R	2009-06-23 11:51:01 UTC (rev 421)
+++ pkg/R/seqTrack.R	2009-06-23 12:17:06 UTC (rev 422)
@@ -212,13 +212,17 @@
 
 
     ## FIND THE COLOR FOR EDGES ##
-    if(is.null(col) & !is.null(support)){
-        opalette <- palette()
-        on.exit(palette(opalette))
+    if(is.null(col)){
+        if(!is.null(support)){
+            opalette <- palette()
+            on.exit(palette(opalette))
 
-        w <- support/max(support,na.rm=TRUE) # support from 0 to 1
-        w <- 1 + ((1-w)*99)
-        col <- w
+            w <- support/max(support,na.rm=TRUE) # support from 0 to 1
+            w <- 1 + ((1-w)*99)
+            col <- w
+        } else{
+            col <- rep("black", length(from))
+        }
     }