[adegenet-commits] r250 - pkg/man

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

Author: jombart
Date: 2009-01-27 12:47:06 +0100 (Tue, 27 Jan 2009)
New Revision: 250

Modified:
   pkg/man/loadingplot.Rd
Log:
Added2 new args in the doc.


Modified: pkg/man/loadingplot.Rd
===================================================================
--- pkg/man/loadingplot.Rd	2009-01-26 18:23:11 UTC (rev 249)
+++ pkg/man/loadingplot.Rd	2009-01-27 11:47:06 UTC (rev 250)
@@ -11,20 +11,25 @@
   variable (loadings) in a given analysis.
 }
 \usage{
-loadingplot(x, threshold=quantile(x,0.75), axis=1, fac=NULL,
-                        lab=names(x), cex.lab=0.7, cex.fac=1, lab.jitter=0,
-                        main="Loading plot", xlab="Variables", ylab="Loadings",\dots)
+loadingplot(x, at=NULL, threshold=quantile(x,0.75), axis=1, fac=NULL, byfac=FALSE,
+            lab=names(x), cex.lab=0.7, cex.fac=1, lab.jitter=0,
+            main="Loading plot", xlab="Variables", ylab="Loadings",\dots)
 
 }
 \arguments{
   \item{x}{either a vector with numeric values to be plotted, or a
     matrix-like object containing numeric values. In such case, the
     \code{x[,axis]} is used as vector of values to be plotted.}
+  \item{at}{an optional numeric vector giving the abscissa at which
+    loadings are plotted. Useful when variates are SNPs with a known
+    position in an alignement.}
   \item{threshold}{a threshold value above which values of x are
     identified. By default, this is the third quartile of x.}
   \item{axis}{an integer indicating the column of x to be plotted; used
     only if x is a matrix-like object.}
   \item{fac}{a factor defining groups of observations.}
+  \item{byfac}{a logical stating whether loadings should be averaged by
+    groups of observations, as defined by \code{fac}.}
   \item{lab}{a character vector giving the labels used to annotate
     values above the threshold.}
   \item{cex.lab}{a numeric value indicating the size of annotations.}