[adegenet-commits] r925 - in pkg: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 22 17:05:40 CEST 2011
Author: jombart
Date: 2011-06-22 17:05:40 +0200 (Wed, 22 Jun 2011)
New Revision: 925
Modified:
pkg/ChangeLog
pkg/DESCRIPTION
pkg/R/auxil.R
pkg/man/adegenet.package.Rd
pkg/man/auxil.Rd
Log:
Everything ready to go.
Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog 2011-06-22 13:14:12 UTC (rev 924)
+++ pkg/ChangeLog 2011-06-22 15:05:40 UTC (rev 925)
@@ -1,3 +1,49 @@
+ CHANGES IN ADEGENET VERSION 1.3-0
+
+
+
+BUG FIXES
+
+ o fixed broken dependencies with hierfstat and graph packages
+ (used to be FAQ #4).
+
+ o fixed a minor bug in loadingplot regarding possible label errors.
+
+NEW FEATURES
+
+ o genome-wide SNP data support using the new class genlight,
+ supported by compiled C routines and parallelized computations on
+ multicore architectures.
+
+ o dedicated find.clusters and dapc methods for genlight objects.
+
+ o read.PLINK to read SNP data with PLINK format into genlight
+ objects.
+
+ o read.snp to read SNP data with adegenet's own format into genlight
+ objects.
+
+ o fasta2genlight to extract SNP from FASTA files into genlight
+ objects.
+
+ o new method 'predict' for DAPC objects, allowing for using
+ supplementary individuals.
+
+ o many new options of DAPC scatterplots (scatter.dapc).
+
+ o new plotting method 'compoplot' for DAPC objects, displaying
+ group memberships in a STRUCTURE-like way... only prettier.
+
+ o many new accessors for the classes genind and genpop.
+
+ o 4 new tutorial vignettes: adegenet-basics, adegenet-dapc,
+ adegenet-spca, adegenet-genomics.
+
+ o last but not least: Ismail Ahmed has joined the project as a
+ developper.
+
+
+
CHANGES IN ADEGENET VERSION 1.2-8
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-06-22 13:14:12 UTC (rev 924)
+++ pkg/DESCRIPTION 2011-06-22 15:05:40 UTC (rev 925)
@@ -1,6 +1,6 @@
Package: adegenet
Version: 1.3-0
-Date: 2010/11/05
+Date: 2011/06/22
Title: adegenet: a R package for the multivariate analysis of genetic markers.
Author: Thibaut Jombart <t.jombart at imperial.ac.uk>
with contributions of: Ismail Ahmed, Peter Solymos
Modified: pkg/R/auxil.R
===================================================================
--- pkg/R/auxil.R 2011-06-22 13:14:12 UTC (rev 924)
+++ pkg/R/auxil.R 2011-06-22 15:05:40 UTC (rev 925)
@@ -70,28 +70,28 @@
-############################
-# Function adegenetTutorial
-############################
-adegenetTutorial <- function(which=c("general","spca")){
- which <- match.arg(which)
- if(which=="general"){
- url <- "http://adegenet.r-forge.r-project.org/files/adegenet.pdf"
- cat("\n")
- cat(" >> Seeking the general tutorial for adegenet.\n")
- cat(" >> Opening url \"",url,"\".\n ", sep="")
- cat("\n")
- browseURL(url)
- }
- if(which=="spca"){
- url <- "http://adegenet.r-forge.r-project.org/files/tutorial-spca.pdf"
- cat("\n")
- cat(" >> Seeking the sPCA tutorial for adegenet.\n")
- cat(" >> Opening url \"",url,"\". \n", sep="")
- cat("\n")
- browseURL(url)
- }
-}
+## ############################
+## # Function adegenetTutorial
+## ############################
+## adegenetTutorial <- function(which=c("basics","spca")){
+## which <- match.arg(which)
+## if(which=="general"){
+## url <- "http://adegenet.r-forge.r-project.org/files/adegenet.pdf"
+## cat("\n")
+## cat(" >> Seeking the general tutorial for adegenet.\n")
+## cat(" >> Opening url \"",url,"\".\n ", sep="")
+## cat("\n")
+## browseURL(url)
+## }
+## if(which=="spca"){
+## url <- "http://adegenet.r-forge.r-project.org/files/tutorial-spca.pdf"
+## cat("\n")
+## cat(" >> Seeking the sPCA tutorial for adegenet.\n")
+## cat(" >> Opening url \"",url,"\". \n", sep="")
+## cat("\n")
+## browseURL(url)
+## }
+## }
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2011-06-22 13:14:12 UTC (rev 924)
+++ pkg/man/adegenet.package.Rd 2011-06-22 15:05:40 UTC (rev 925)
@@ -5,24 +5,33 @@
\docType{package}
\title{The adegenet package}
-\description{This package is devoted to the multivariate analysis of
+\description{
+
+ This package is devoted to the multivariate analysis of
genetic markers data. These data can be codominant markers (e.g. microsatellites) or
presence/absence data (e.g. AFLP), and have any level of ploidy.
- 'adegenet' defines two formal (S4) classes:\cr
+ 'adegenet' defines three formal (S4) classes:\cr
- \linkS4class{genind}: a class for data of individuals ("genind" stands for genotypes-individuals).\cr
- - \linkS4class{genpop}: a class for data of groups of individuals ("genpop" stands for genotypes-populations)\cr
- For more information about these classes, type "class ? genind" or
- "class ? genpop".\cr
+ - \linkS4class{genpop}: a class for data of groups of individuals
+ ("genpop" stands for genotypes-populations)\cr
+ - \linkS4class{genlight}: a class for genome-wide SNP data\cr
- Both types of objects store information from molecular markers in a matrix (\$tab slot),
- that can be directly analyzed using multivariate methods such as
- Principal Component Analysis, Correspondance Analysis, etc. See the
- "dudi.[...]" methods in the \code{ade4} package. Moreover, this
- package offers methods for manipulating and analyzing information
- coming from genetic markers (see below). \cr
+ For more information about these classes, type "class ? genind",
+ "class ? genpop", or "?genlight".\cr
+ Essential functionalities of the package are presented througout 4
+ tutorial vignettes, accessible using \code{vignette("name-below", package="adegenet")}:\cr
+ - adegenet-basics: introduction to the package.\cr
+ - adegenet-spca: multivariate analysis of spatial genetic patterns.\cr
+ - adegenet-dapc: population structure and group assignment using DAPC.\cr
+ - adegenet-genomics: introduction to the class \linkS4class{genlight}
+ for the handling and analysis of genome-wide SNP data.\cr
+ Important functions are also summarized below.\cr
+
+
=== IMPORTING DATA ===\cr
+ = TO GENIND OBJECTS = \cr
\code{adegenet} imports data to \linkS4class{genind} object from the
following softwares:\cr
- STRUCTURE: see \code{\link{read.structure}}\cr
@@ -32,6 +41,8 @@
To import data from any of these formats, you can also use the general
function \code{\link{import2genind}}.\cr
+ In addition, it can extract polymorphic sites from nucleotide and
+ amino-acid alignments:\cr
- DNA files: use \code{\link[ape]{read.dna}} from the ape package,
and then extract SNPs from DNA alignments using
\code{\link{DNAbin2genind}}. \cr
@@ -47,7 +58,15 @@
this, use \code{\link{df2genind}}. Note that \code{\link{df2genind}}
can be used for any level of ploidy.\cr
+ = TO GENLIGHT OBJECTS = \cr
+ SNP data can be read from the following formats:\cr
+ - PLINK: see function \code{\link{read.PLINK}}\cr
+ - .snp (adegenet's own format): see function \code{\link{read.snp}}\cr
+ SNP can also be extracted from aligned DNA sequences with the fasta
+ format, using \code{\link{fasta2genlight}}\cr
+
+
=== EXPORTING DATA ===\cr
\code{adegenet} exports data from \linkS4class{genind} object to
formats recognized by other R packages:\cr
@@ -65,7 +84,8 @@
\linkS4class{genpop} objects\cr
- \code{\link{genind2genpop}}: convert a \linkS4class{genind} object
to a \linkS4class{genpop} \cr
- - \code{\link{seploc}}: creates one object per marker \cr
+ - \code{\link{seploc}}: creates one object per marker; for
+ \linkS4class{genlight} objects, creates blocks of SNPs.\cr
- \code{\link{seppop}}: creates one object per population \cr
- \code{\link{na.replace}}: replaces missing data (NA) in an
approriate way \cr
@@ -90,8 +110,6 @@
- \code{\link{HWE.test.genind}}: performs HWE test for all
populations and loci combinations \cr
- \code{\link{pairwise.fst}}: computes simple pairwise Fst between populations\cr
- % - \code{\link{gstat.randtest}}: performs a Monte Carlo test of Goudet's G statistic, measuring
- % population structure (based on \code{\link[hierfstat]{g.stats.glob}} package \code{hierfstat}).\cr
- \code{\link{dist.genpop}}: computes 5 genetic distances among populations. \cr
- \code{\link{monmonier}}: implementation of the Monmonier algorithm,
used to seek genetic boundaries among individuals or
@@ -121,8 +139,11 @@
- \code{\link{seqTrack}}: implements the SeqTrack algorithm for
recontructing transmission trees of pathogens (Jombart et al.,
2010) .\cr
+ \code{\link{glPca}}: implements PCA for \linkS4class{genlight}
+ objects.\cr
+
=== GRAPHICS ===\cr
- \code{\link{colorplot}}: plots points with associated values for up
to three variables represented by colors using the RGB system;
@@ -130,6 +151,9 @@
- \code{\link{loadingplot}}: plots loadings of variables. Useful for
representing the contribution of alleles to a given principal
component in a multivariate method. \cr
+ - \code{\link{scatter.dapc}}: scatterplots for DAPC results.\cr
+ - \code{\link{compoplot}}: plots membership probabilities from a DAPC
+ object. \cr
=== SIMULATING DATA ===\cr
@@ -138,6 +162,7 @@
storing full genomes. \cr
- \code{\link{haploPop}}: simulates populations of haplotypes, using
different population dynamics, storing SNPs (under development). \cr
+ - \code{\link{glSim}}: simulates simple \linkS4class{genlight} objects.\cr
=== DATASETS ===\cr
@@ -154,10 +179,7 @@
For more information, visit the adegenet website by typing
\code{adegenetWeb()}.\cr
- Tutorials are available on the adegenet website, or by typing
- \code{adegenetTutorial()}.\cr
-
To cite adegenet, please use the reference given by
\code{citation("adegenet")} (or see reference below).
}
@@ -166,15 +188,15 @@
Package: \tab adegenet\cr
Type: \tab Package\cr
Version: \tab 1.3-0\cr
- Date: \tab 2011-06-?? \cr
+ Date: \tab 2011-06-22 \cr
License: \tab GPL (>=2)
- }
+ }
}
\author{
Thibaut Jombart <t.jombart at imperial.ac.uk>\cr
with contributions of: Ismail Ahmed, Peter Solymos\cr
and contributed datasets from: Katayoun Moazami-Goudarzi, Denis Laloë,
- Dominique Pontier, Daniel Maillard, Francois Balloux
+ Dominique Pontier, Daniel Maillard, Francois Balloux.
}
\references{
Jombart T. (2008) adegenet: a R package for the multivariate analysis
@@ -189,13 +211,13 @@
Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease
outbreaks from genetic data: a graph approach. \emph{Heredity}. doi:
10.1038/hdy.2010.78.\cr
-
+
Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. Revealing
cryptic spatial patterns in genetic variability by a new multivariate
method. \emph{Heredity}, \bold{101}, 92--103.\cr
See adegenet website: \url{http://adegenet.r-forge.r-project.org/}\cr
-
+
Please post your questions on 'the adegenet forum': adegenet-forum at lists.r-forge.r-project.org
}
Modified: pkg/man/auxil.Rd
===================================================================
--- pkg/man/auxil.Rd 2011-06-22 13:14:12 UTC (rev 924)
+++ pkg/man/auxil.Rd 2011-06-22 15:05:40 UTC (rev 925)
@@ -2,7 +2,7 @@
\docType{methods}
\name{Auxiliary functions}
\alias{adegenetWeb}
-\alias{adegenetTutorial}
+%\alias{adegenetTutorial}
\alias{checkType}
\alias{.rmspaces}
\alias{.genlab}
@@ -12,10 +12,9 @@
\alias{transp}
\title{ Utilities functions for adegenet}
\description{
- These functions are mostly used internally in adegenet. The notable
- exceptions are \code{adegenetWeb} which opens the adegenet website in
- the default navigator, \code{adegenetTutorial} which opens online
- tutorials for adegenet, and a few auxiliary graphical functions.\cr
+ These functions are mostly auxiliary procedures used internally in
+ adegenet, with the exception of \code{adegenetWeb}, which opens the
+ adegenet website in the default navigator.\cr
The other functions are:\cr
- \code{checkType}: checks the type of markers being used in a
@@ -30,7 +29,6 @@
}
\usage{
adegenetWeb()
-adegenetTutorial(which=c("general","spca"))
.genlab(base, n)
corner(text, posi="topleft", inset=0.1, \dots)
num2col(x, col.pal=heat.colors, reverse=FALSE,
@@ -38,8 +36,6 @@
transp(col, alpha=.5)
}
\arguments{
- \item{which}{a character string being "general" or "spca", indicating
- which tutorial should be opened.}
\item{base}{a character string forming the base of the labels}
\item{n}{the number of labels to generate}
\item{text}{a character string to be added to the plot}
@@ -68,13 +64,17 @@
## this opens the adegenet website
adegenetWeb()
-## this opens the general tutorial for adegenet
-adegenetTutorial()
-
-## this opens the sPCA tutorial for adegenet
-adegenetTutorial("spca")
}
.genlab("Locus-",11)
+
+## transparent colors using "transp"
+plot(rnorm(1000), rnorm(1000), col=transp("blue",.3), pch=20, cex=4)
+
+
+## numeric values to color using num2col
+plot(1:100, col=num2col(1:100), pch=20, cex=4)
+plot(1:100, col=num2col(1:100, col.pal=rainbow), pch=20, cex=4)
+
}
\keyword{manip}
\ No newline at end of file
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