[adegenet-commits] r885 - in pkg: R inst/doc inst/doc/figs

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun May 29 15:26:00 CEST 2011 

Author: jombart
Date: 2011-05-29 15:25:59 +0200 (Sun, 29 May 2011)
New Revision: 885

Added:
   pkg/inst/doc/adegenet-dapc.pdf
Modified:
   pkg/R/dapc.R
   pkg/R/loadingplot.R
   pkg/inst/doc/adegenet-dapc.Rnw
   pkg/inst/doc/figs/-006.pdf
   pkg/inst/doc/figs/-010.pdf
   pkg/inst/doc/figs/-011.pdf
   pkg/inst/doc/figs/-012.pdf
   pkg/inst/doc/figs/-013.pdf
   pkg/inst/doc/figs/-015.pdf
   pkg/inst/doc/figs/-016.pdf
   pkg/inst/doc/figs/-018.pdf
Log:
Fixed issue with loadingplot.
Vignette DAPC nearly complete.


Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R	2011-05-27 16:45:15 UTC (rev 884)
+++ pkg/R/dapc.R	2011-05-29 13:25:59 UTC (rev 885)
@@ -516,13 +516,13 @@
 
         ## add minimum spanning tree if needed
         if(mstree && require(ade4)){
-            meanposi <- apply(dapc1$tab,2, tapply, dapc1$grp, mean)
+            meanposi <- apply(x$tab,2, tapply, x$grp, mean)
             D <- dist(meanposi)^2
             tre <- mstree(D)
-            x0 <- dapc1$grp.coord[tre[,1], axes[1]]
-            y0 <- dapc1$grp.coord[tre[,1], axes[2]]
-            x1 <- dapc1$grp.coord[tre[,2], axes[1]]
-            y1 <- dapc1$grp.coord[tre[,2], axes[2]]
+            x0 <- x$grp.coord[tre[,1], axes[1]]
+            y0 <- x$grp.coord[tre[,1], axes[2]]
+            x1 <- x$grp.coord[tre[,2], axes[1]]
+            y1 <- x$grp.coord[tre[,2], axes[2]]
             segments(x0, y0, x1, y1, lwd=lwd, lty=lty, col=segcol)
         }
 

Modified: pkg/R/loadingplot.R
===================================================================
--- pkg/R/loadingplot.R	2011-05-27 16:45:15 UTC (rev 884)
+++ pkg/R/loadingplot.R	2011-05-29 13:25:59 UTC (rev 885)
@@ -61,23 +61,27 @@
     }
 
     ## annotate variables that are above the threshold
-    x.ann <- at[x > threshold]
-    x.ann <- jitter(x.ann,fac=lab.jitter)
+    if(sum(x > threshold)>0){
+        x.ann <- at[x > threshold]
+        x.ann <- jitter(x.ann,fac=lab.jitter)
 
-    y.ann <- x[x > threshold] + y.offset
-    y.ann <- jitter(y.ann,fac=lab.jitter)
+        y.ann <- x[x > threshold] + y.offset
+        y.ann <- jitter(y.ann,fac=lab.jitter)
 
-    txt.ann <- lab[x > threshold]
-    text(x=x.ann, y=y.ann, label=txt.ann, cex=cex.lab, srt=srt, adj=adj)
-
+        txt.ann <- lab[x > threshold]
+        text(x=x.ann, y=y.ann, label=txt.ann, cex=cex.lab, srt=srt, adj=adj)
+    
     ## indicate the threshold
     abline(h=threshold, col="grey")
 
     ## build the result
+    
     res <- list(threshold=threshold,
                 var.names=txt.ann,
                 var.idx=which(x > threshold),
                 var.values=x[x > threshold])
     return(invisible(res))
+    }
 
+    return(NULL) # if no point above threshold
 } # end loadingplot

Modified: pkg/inst/doc/adegenet-dapc.Rnw
===================================================================
--- pkg/inst/doc/adegenet-dapc.Rnw	2011-05-27 16:45:15 UTC (rev 884)
+++ pkg/inst/doc/adegenet-dapc.Rnw	2011-05-29 13:25:59 UTC (rev 885)
@@ -439,12 +439,13 @@
 The first discriminant function shows the temporal evolution of the influenza virus, while the
 second one shows the originality of 2006 strains.
 <<fig=TRUE>>=
+myPal <- colorRampPalette(c("blue","gold","red"))
 scatter(dapc.flu, col=transp(myPal(6)), ratio=0, cell=0, cex=2, bg="white",cstar=0)
 @
 
 We can assess which alleles most highlight the originality of 2006 using \texttt{loadingplot}:
 <<fig=TRUE>>=
-temp <- loadingplot(dapc.flu$var.contr, thres=.5)
+temp <- loadingplot(dapc.flu$var.contr, thres=.05)
 @
 
 

Added: pkg/inst/doc/adegenet-dapc.pdf
===================================================================
--- pkg/inst/doc/adegenet-dapc.pdf	                        (rev 0)
+++ pkg/inst/doc/adegenet-dapc.pdf	2011-05-29 13:25:59 UTC (rev 885)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 885

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