[adegenet-commits] r620 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon May 10 17:34:05 CEST 2010
Author: jombart
Date: 2010-05-10 17:34:05 +0200 (Mon, 10 May 2010)
New Revision: 620
Modified:
pkg/R/seqTrack.R
pkg/man/seqTrack.Rd
Log:
Done with arguments.
Modified: pkg/R/seqTrack.R
===================================================================
--- pkg/R/seqTrack.R 2010-05-10 15:12:33 UTC (rev 619)
+++ pkg/R/seqTrack.R 2010-05-10 15:34:05 UTC (rev 620)
@@ -24,15 +24,10 @@
UseMethod("get.likelihood")
}
-get.likelihood.seqTrack.default <- function(...){
- cat("Method not implemented.")
- return()
-}
-
########################
## seqTrack - basic version
########################
@@ -163,8 +158,8 @@
################
## plotSeqTrack
################
-plotSeqTrack <- function(x, xy, useArrows=TRUE, annot=TRUE, labels=NULL,
- col=NULL, bg="grey", add=FALSE, quiet=FALSE, dateRange=NULL,
+plotSeqTrack <- function(x, xy, use.arrows=TRUE, annot=TRUE, labels=NULL,
+ col=NULL, bg="grey", add=FALSE, quiet=FALSE, date.range=NULL,
plot=TRUE,...){
## CHECKS ##
@@ -215,21 +210,21 @@
## HANDLE RANGE OF DATES ##
- if(!is.null(dateRange)){
+ if(!is.null(date.range)){
- if(is.character(dateRange)){
- msg <- paste("dateRange is a character vector; " ,
+ if(is.character(date.range)){
+ msg <- paste("date.range is a character vector; " ,
"please convert it as dates using 'as.POSIXct'" ,
"\n(making sure dates are given as 'YYYY/MM/DD' or 'YYYY-MM-DD').", sep="")
stop(msg)
}
- if(any(is.na(dateRange))){
- stop("NA in dateRange")
+ if(any(is.na(date.range))){
+ stop("NA in date.range")
}
dates <- x$date
- toKeep <- (dates > min(dateRange)) & (dates < max(dateRange))
+ toKeep <- (dates > min(date.range)) & (dates < max(date.range))
if(sum(toKeep)==0) {
if(!quiet) cat("\nNo item in the specified date range.\n")
return(NULL)
@@ -263,7 +258,7 @@
## PLOTTING ##
if(plot){
## ARROWS
- if(useArrows){
+ if(use.arrows){
## handle segments/arrows with length 0 ##
nullLength <- (abs(x.from-x.to)<1e-10) & (abs(y.from-y.to)<1e-10)
Modified: pkg/man/seqTrack.Rd
===================================================================
--- pkg/man/seqTrack.Rd 2010-05-10 15:12:33 UTC (rev 619)
+++ pkg/man/seqTrack.Rd 2010-05-10 15:34:05 UTC (rev 620)
@@ -8,7 +8,6 @@
% \alias{optimize.seqTrack.default}
\alias{get.likelihood}
\alias{get.likelihood.seqTrack}
-\alias{get.likelihood.seqTrack.default}
\alias{seqTrack-class}
% \alias{get.result.by}
% \alias{get.consensus}
@@ -35,15 +34,14 @@
\method{seqTrack}{matrix}(x, x.names, x.dates, best = c("min", "max"), prox.mat = NULL,
mu = NULL, haplo.length = NULL, \dots)
-plotSeqTrack(x, xy, useArrows = TRUE, annot = TRUE, labels = NULL,
- dateRange = NULL, col = NULL, bg = "grey", add = FALSE, quiet = FALSE,
- support = NULL, support.thres = 0.5, timeorder.thres = NULL,
- mu = NULL, seq.length = NULL, col.pal = heat.colors, plot = TRUE, \dots)
+plotSeqTrack(x, xy, use.arrows=TRUE, annot=TRUE, labels=NULL,
+ col=NULL, bg="grey", add=FALSE, quiet=FALSE, date.range=NULL,
+ plot=TRUE, \dots)
}
\arguments{
- \item{x}{for seqTrack, a matrix giving weights to pairs of ancestries such that
- x[i,j] is the weight of 'i ancestor of j'. For plotSeqTrack, a
- seqTrack object.}
+ \item{x}{for seqTrack, a matrix giving weights to pairs of ancestries
+ such that x[i,j] is the weight of 'i ancestor of j'. For
+ plotSeqTrack, a seqTrack object.}
\item{seq.names}{a character vector giving the labels of the haplotypes/genotypes}
\item{seq.dates}{a vector of collection dates for the sampled
haplotypes/genotypes. Dates must have the POSIXct format. See
@@ -66,51 +64,26 @@
\item{haplo.length}{(optional) the length of analysed sequences in
number of nucleotides. When 'x' contains numbers of mutations, used
to resolve ties using a maximum likelihood approach (requires
- \code{mu} to be provided).}
+ \code{mu} to be provided).}
\item{xy}{spatial coordinates of the sampled haplotypes/genotypes.}
- \item{useArrows}{a logical indicating whether arrows should be used to
+ \item{use.arrows}{a logical indicating whether arrows should be used to
represented ancestries (pointing from ancestor to descendent, TRUE),
or whether segments shall be used (FALSE).}
\item{annot}{a logical indicating whether arrows or segments
representing ancestries should be annotated (TRUE) or not (FALSE).}
\item{labels}{a character vector containing annotations of the
ancestries. If left empty, ancestries are annotated by the descendent.}
- \item{dateRange}{a vector of length two with POSIXct format indicating
- the time window for which ancestries should be displayed.}
\item{col}{a vector of colors to be used for plotting ancestries.}
\item{bg}{a color to be used as background.}
\item{add}{a logical stating whether the plot should be added to
current figure (TRUE), or drawn as a new plot (FALSE, default).}
\item{quiet}{a logical stating whether messages other than errors
should be displayed (FALSE, default), or hidden (TRUE).}
- \item{support}{an optional vector of numbers between 0 and 1
- indicating the support for each ancestry. If provided and if
- \code{col} is left empty, ancestries are represented with colors
- indicating the support.}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
-
- \item{col}{}
- \item{bg}{}
- \item{add}{}
- \item{\dots}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
- \item{}{}
+ \item{date.range}{a vector of length two with POSIXct format indicating
+ the time window for which ancestries should be displayed.}
+ \item{plot}{a logical stating whether a plot should be drawn (TRUE,
+ default), or not (FALSE). In all cases, the
+ function invisibly returns plotting information.}
}
\author{
Thibaut Jombart \email{t.jombart at imperial.ac.uk}
@@ -118,4 +91,29 @@
\references{
Jombart T, Eggo R, Dodd P, Balloux F (accepted) Reconstructing disease
outbreaks from genetic data: a graph approach. Heredity.
+}
+\value{
+ === output of seqTrack ===
+ seqTrack function returns data.frame with the class \code{seqTrack},
+ in which each row is an inferred ancestry described by the following columns:
+ - id: indices identifying haplotypes/genotypes
+ - ances: index of the inferred ancestor
+ - weight: weight of the inferred ancestries
+ - date: date of the haplotype/genotype
+ - ances.date: date of the ancestor
+
+ === output of plotSeqTrack ===
+ This graphical function invisibly returns the coordinates of the
+ arrows/segments drawn and their colors, as a data.frame.
+}
+\details{
+ === Maximum parsimony genealogies ===
+
+ === Likelihood of observed genetic differentiation ===
+ === Converting seqTrack objects to graphs ===
+
+
+}
+\seealso{
+ \code{\link{get.likelihood.seqTrack}}
}
\ No newline at end of file
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