[adegenet-commits] r917 - in pkg/inst/doc: . figs
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 16 18:56:36 CEST 2011
Author: jombart
Date: 2011-06-16 18:56:36 +0200 (Thu, 16 Jun 2011)
New Revision: 917
Modified:
pkg/inst/doc/adegenet-basics.Rnw
pkg/inst/doc/adegenet-basics.aux
pkg/inst/doc/adegenet-basics.log
pkg/inst/doc/adegenet-basics.out
pkg/inst/doc/adegenet-basics.pdf
pkg/inst/doc/adegenet-basics.tex
pkg/inst/doc/adegenet-basics.toc
pkg/inst/doc/figs/base-040.pdf
pkg/inst/doc/figs/base-063.pdf
pkg/inst/doc/figs/base-065.pdf
pkg/inst/doc/figs/base-068.pdf
pkg/inst/doc/figs/base-070.pdf
pkg/inst/doc/figs/base-071.pdf
pkg/inst/doc/figs/base-072.pdf
pkg/inst/doc/figs/base-073.pdf
pkg/inst/doc/figs/base-074.pdf
pkg/inst/doc/figs/base-075.pdf
pkg/inst/doc/figs/base-077.pdf
pkg/inst/doc/figs/base-078.pdf
pkg/inst/doc/figs/base-080.pdf
pkg/inst/doc/figs/base-082.pdf
pkg/inst/doc/figs/base-083.pdf
pkg/inst/doc/figs/base-098.pdf
pkg/inst/doc/figs/base-099.pdf
pkg/inst/doc/figs/base-caexpl.pdf
pkg/inst/doc/figs/base-mon1.pdf
pkg/inst/doc/figs/base-mon4.pdf
pkg/inst/doc/figs/base-mon6.pdf
pkg/inst/doc/figs/base-njAA.pdf
pkg/inst/doc/figs/base-pcaaflp.pdf
pkg/inst/doc/figs/base-sumry.pdf
Log:
Added some missing refs.
Modified: pkg/inst/doc/adegenet-basics.Rnw
===================================================================
--- pkg/inst/doc/adegenet-basics.Rnw 2011-06-16 16:11:07 UTC (rev 916)
+++ pkg/inst/doc/adegenet-basics.Rnw 2011-06-16 16:56:36 UTC (rev 917)
@@ -75,7 +75,7 @@
This tutorial introduces some basic functionalities of the \textit{adegenet} package for R \cite{np145}.
The purpose of this package is to provide tools for handling, analysing and simulating genetic
markers data, with an emphasis on multivariate approaches and exploratory methods.
-Standard multivariate analyses are implemented in the \textit{ade4} package \cite{tj311}, of which
+Standard multivariate analyses are implemented in the \textit{ade4} package \cite{tj548}, of which
\textit{adegenet} was originally an extension.
However, the package has since grown methods of its own such as the Discriminant Analysis of
Principal Components (DAPC, \cite{tjart19}), the spatial Principal Components Analysis (sPCA,
@@ -101,6 +101,7 @@
+\newpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Getting started}
@@ -114,7 +115,6 @@
Before going further, we shall make sure that \textit{adegenet} is weel installed
on the computer.
Current version of the package is \Sexpr{packageDescription("adegenet", fields = "Version")}.
-
Make sure you have a recent version ($\geq 2.13.0$) of R by typing:
<<>>=
R.version.string
@@ -223,6 +223,7 @@
+\newpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Object classes}
@@ -411,6 +412,7 @@
+\newpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Importing/exporting data}
@@ -614,7 +616,7 @@
\\
-DNA sequences can be read into R using the ape package \cite{tj527,np83}, and
+DNA sequences can be read into R using the ape package \cite{tj527}, and
imported into adegenet using \texttt{DNAbin2genind}.
There are several ways ape can be used to read in DNA sequences.
The easiest one is reading data from a usual format such as FASTA or Clustal using \texttt{read.dna}.
@@ -816,6 +818,7 @@
+\newpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Basics of data analysis}
@@ -1137,6 +1140,7 @@
<<fig=TRUE>>=
plot(F$FRBTSAL9266, main=paste("Inbreeding of individual",names(F)), xlab="Inbreeding (F)", ylab="Probability density")
@
+
\noindent Indeed, this individual shows subsequent inbreeding, with about 50\% chances of being
homozygote through inheritance from a common ancestor of its parents.
@@ -1145,6 +1149,7 @@
+\newpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Multivariate analysis}
@@ -1289,7 +1294,7 @@
add.scatter.eig(pca1$eig[1:20], 3,1,2)
@
-However, this figure can largely be improved.
+\noindent However, this figure can largely be improved.
First, we can use \texttt{s.class} to represent both the genotypes and inertia ellipses for populations.
<<fig=T>>=
s.class(pca1$li, pop(obj),lab=obj$pop.names)
@@ -1304,7 +1309,8 @@
title("PCA of microbov dataset\naxes 1-3")
add.scatter.eig(pca1$eig[1:20],nf=3,xax=1,yax=3)
@
-Overall, all breeds seem well differentiated.
+
+\noindent Overall, all breeds seem well differentiated.
~\\
However, we can yet improve these scatterplots, which are fortunately easy to customize.
@@ -1326,10 +1332,12 @@
title("PCA of microbov dataset\naxes 1-2")
abline(v=0,h=0,col="grey", lty=2)
@
-Colors are based on the first three PCs of the PCA, recoded respectively on the red, green, and blue channel.
+
+\noindent Colors are based on the first three PCs of the PCA, recoded respectively on the red, green, and blue channel.
In this figure, the genetic diversity is represented in two redundant ways: by the distances
(further away = more genetically different), and by the colors (more different colors = more
genetically different).
+\\
We can represent the diversity on the third axis similarly:
<<fig=TRUE>>=
@@ -1424,6 +1432,7 @@
\SweaveOpts{eval=TRUE}
+\newpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Spatial analysis}
@@ -1479,9 +1488,10 @@
<<fig=TRUE>>=
plot(ibd)
@
-This time there is a clear isolation by distance pattern.
+\noindent This time there is a clear isolation by distance pattern.
+
% % % % % % % % % % % % % % % % % % % % %
\subsubsection{Cline or distant patches?}
% % % % % % % % % % % % % % % % % % % % %
@@ -1546,10 +1556,10 @@
summary(sim2pop$pop)
temp <- sim2pop$pop
-levels(temp) <- 3:4
+levels(temp) <- c(3,5)
temp <- as.numeric(as.character(temp))
plot(sim2pop$other$xy,pch=temp,cex=1.5,xlab='x',ylab='y')
-legend("topright",leg=c("Pop A", "Pop B"),pch=3:4)
+legend("topright",leg=c("Pop A", "Pop B"),pch=c(3,5))
@
There are two sampled populations in this dataset, with inequal sample sizes (100 and 30).
@@ -1667,10 +1677,10 @@
<<fig=TRUE>>=
plot(mon1,add.arrows=FALSE,bwd=8)
temp <- sim2pop$pop
-levels(temp) <- 3:4
+levels(temp) <- c(3,5)
temp <- as.numeric(as.character(temp))
points(sim2pop$other$xy,pch=temp,cex=1.3)
-legend("topright",leg=c("Pop A", "Pop B"),pch=3:4)
+legend("topright",leg=c("Pop A", "Pop B"),pch=c(3,5))
@
\noindent Not too bad...
@@ -1679,8 +1689,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{How to simulate hybridization?}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Simulating hybridization}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The function \texttt{hybridize} allows to simulate hybridization between
individuals from two distinct genetic pools, or more broadly between
two \texttt{genind} objects.
@@ -1714,14 +1726,9 @@
-
+\newpage
\begin{thebibliography}{9}
-\bibitem{tjart19}
- Jombart T, Devillard S and Balloux, F (2010).
- Discriminant analysis of principal components: a new method for the analysis of genetically structured populations.
- \textit{BMC Genetics} 11: 94.
-
\bibitem{tjart05}
Jombart, T. (2008) adegenet: a R package for the multivariate
analysis of genetic markers. \textit{Bioinformatics} 24: 1403-1405.
@@ -1731,14 +1738,46 @@
statistical computing. R Foundation for Statistical Computing,
Vienna, Austria. ISBN 3-900051-07-0.
+\bibitem{tj548}
+ Dray S and Dufour A-B (2007) The ade4 package: implementing the duality diagram for ecologists. \textit{Journal of Statistical Software} 22: 1-20.
+
+\bibitem{tjart19}
+ Jombart T, Devillard S and Balloux, F (2010).
+ Discriminant analysis of principal components: a new method for the analysis of genetically structured populations.
+ \textit{BMC Genetics} 11: 94.
+
+\bibitem{tjart04}
+ Jombart T, Devillard S, Dufour A-B and Pontier D (2008) Revealing cryptic spatial
+ patterns in genetic variability by a new multivariate method. \textit{Heredity} 101: 92-103.
+
+\bibitem{tjart20}
+ Jombart T, Eggo RM, Dodd PJ and Balloux F (2010) Reconstructing disease outbreaks from genetic
+ data: a graph approach. \textit{Heredity} 106: 383-390.
+
\bibitem{tjart10}
Jombart T, Pontier D and Dufour A-B (2009) Genetic markers in the playground of multivariate analysis.
\textit{Heredity} 102: 330-341.
-\bibitem{tjart04}
-Jombart T, Devillard S, Dufour A-B and Pontier D (2008) Revealing cryptic spatial patterns in genetic variability by a new multivariate method.
-\textit{Heredity} 101: 92-103.
+\bibitem{tj527}
+ Paradis E, Claude J, and Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language.
+ \textit{Bioinformatics}: 20, 289-290.
+\bibitem{np160}
+ Charif D, and Lobry J (2007) SeqinR 1.0-2: a contributed package to the R project for statistical
+ computing devoted to biological sequences retrieval and analysis. \textit{in} Structural approaches to sequence evolution: Molecules, networks, populations, \textit{Springer Verlag}, 207-232.
+
+\bibitem{tj814}
+ Nei M (1973) Analysis of gene diversity in subdivided populations. \textit{Proc Natl Acad Sci USA} 70: 3321-3323.
+
+
+\bibitem{tj433}
+ Monmonier M (1973) Maximum-difference barriers: an alternative numerical regionalization method. \textit{Geographical Analysis} 3: 245-261.
+
+\bibitem{np120}
+ Manni F, Guerard E and Heyer E (2004) Geographic patterns of (genetic, morphologic, linguistic)
+ variation: how barriers can be detected by "Monmonier's algorithm". \textit{Human Biology} 76: 173-190.
+
+
\end{thebibliography}
\end{document}
Modified: pkg/inst/doc/adegenet-basics.aux
===================================================================
--- pkg/inst/doc/adegenet-basics.aux 2011-06-16 16:11:07 UTC (rev 916)
+++ pkg/inst/doc/adegenet-basics.aux 2011-06-16 16:56:36 UTC (rev 917)
@@ -14,55 +14,61 @@
\citation{tjart05}
\citation{np145}
\citation{np145}
-\citation{tj311}
+\citation{tj548}
\citation{tjart19}
\citation{tjart04}
\citation{tjart20}
\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{3}{section.1}}
-\@writefile{toc}{\contentsline {section}{\numberline {2}Getting started}{3}{section.2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Installing the package}{3}{subsection.2.1}}
\citation{tjart04}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Getting started}{4}{section.2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Installing the package}{4}{subsection.2.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Getting help}{4}{subsection.2.2}}
-\@writefile{toc}{\contentsline {section}{\numberline {3}Object classes}{5}{section.3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}genind objects}{5}{subsection.3.1}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}genpop objects}{9}{subsection.3.2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.3}Using accessors}{10}{subsection.3.3}}
-\@writefile{toc}{\contentsline {section}{\numberline {4}Importing/exporting data}{12}{section.4}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Importing data from GENETIX, STRUCTURE, FSTAT, Genepop}{12}{subsection.4.1}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Importing data from other software}{12}{subsection.4.2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.3}Handling presence/absence data}{14}{subsection.4.3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.4}SNPs data}{17}{subsection.4.4}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}Object classes}{6}{section.3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}genind objects}{6}{subsection.3.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}genpop objects}{10}{subsection.3.2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.3}Using accessors}{11}{subsection.3.3}}
+\@writefile{toc}{\contentsline {section}{\numberline {4}Importing/exporting data}{13}{section.4}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Importing data from GENETIX, STRUCTURE, FSTAT, Genepop}{13}{subsection.4.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Importing data from other software}{13}{subsection.4.2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.3}Handling presence/absence data}{15}{subsection.4.3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.4}SNPs data}{18}{subsection.4.4}}
\citation{tj527}
-\citation{np83}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.5}Extracting polymorphism from DNA sequences}{18}{subsection.4.5}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5}Extracting polymorphism from DNA sequences}{19}{subsection.4.5}}
\citation{np160}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.6}Extracting polymorphism from proteic sequences}{19}{subsection.4.6}}
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-\@writefile{toc}{\contentsline {section}{\numberline {5}Basics of data analysis}{26}{section.5}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {5.1}Manipulating data}{26}{subsection.5.1}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {5.2}Using summaries}{30}{subsection.5.2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {5.3}Testing for Hardy-Weinberg equilibrium}{32}{subsection.5.3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.6}Extracting polymorphism from proteic sequences}{20}{subsection.4.6}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.7}Using genind/genpop constructors}{24}{subsection.4.7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.8}Exporting data}{25}{subsection.4.8}}
+\@writefile{toc}{\contentsline {section}{\numberline {5}Basics of data analysis}{27}{section.5}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.1}Manipulating data}{27}{subsection.5.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.2}Using summaries}{31}{subsection.5.2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.3}Testing for Hardy-Weinberg equilibrium}{33}{subsection.5.3}}
\citation{tj814}
-\@writefile{toc}{\contentsline {subsection}{\numberline {5.4}Measuring and testing population structure (a.k.a F statistics)}{33}{subsection.5.4}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {5.5}Estimating inbreeding}{34}{subsection.5.5}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.4}Measuring and testing population structure (a.k.a F statistics)}{34}{subsection.5.4}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.5}Estimating inbreeding}{35}{subsection.5.5}}
\citation{tjart10}
-\@writefile{toc}{\contentsline {section}{\numberline {6}Multivariate analysis}{37}{section.6}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {6.1}General overview}{37}{subsection.6.1}}
\citation{tjart19}
\citation{tjart04}
-\@writefile{toc}{\contentsline {subsection}{\numberline {6.2}Performing a Principal Component Analysis on \texttt {genind} objects}{39}{subsection.6.2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {6.3}Performing a Correspondance Analysis on \texttt {genpop} objects}{47}{subsection.6.3}}
-\@writefile{toc}{\contentsline {section}{\numberline {7}Spatial analysis}{50}{section.7}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {7.1}Isolation by distance}{50}{subsection.7.1}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {7.1.1}Testing isolation by distance}{50}{subsubsection.7.1.1}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {7.1.2}Cline or distant patches?}{53}{subsubsection.7.1.2}}
+\@writefile{toc}{\contentsline {section}{\numberline {6}Multivariate analysis}{39}{section.6}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {6.1}General overview}{39}{subsection.6.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {6.2}Performing a Principal Component Analysis on \texttt {genind} objects}{41}{subsection.6.2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {6.3}Performing a Correspondance Analysis on \texttt {genpop} objects}{48}{subsection.6.3}}
+\@writefile{toc}{\contentsline {section}{\numberline {7}Spatial analysis}{52}{section.7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {7.1}Isolation by distance}{52}{subsection.7.1}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {7.1.1}Testing isolation by distance}{52}{subsubsection.7.1.1}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {7.1.2}Cline or distant patches?}{54}{subsubsection.7.1.2}}
\citation{tj433}
\citation{np120}
-\@writefile{toc}{\contentsline {subsection}{\numberline {7.2}Using Monmonier's algorithm to define genetic boundaries}{54}{subsection.7.2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {7.3}How to simulate hybridization?}{63}{subsection.7.3}}
-\bibcite{tjart19}{1}
-\bibcite{tjart05}{2}
-\bibcite{np145}{3}
-\bibcite{tjart10}{4}
+\@writefile{toc}{\contentsline {subsection}{\numberline {7.2}Using Monmonier's algorithm to define genetic boundaries}{56}{subsection.7.2}}
+\@writefile{toc}{\contentsline {section}{\numberline {8}Simulating hybridization}{65}{section.8}}
+\bibcite{tjart05}{1}
+\bibcite{np145}{2}
+\bibcite{tj548}{3}
+\bibcite{tjart19}{4}
\bibcite{tjart04}{5}
+\bibcite{tjart20}{6}
+\bibcite{tjart10}{7}
+\bibcite{tj527}{8}
+\bibcite{np160}{9}
+\bibcite{tj814}{10}
+\bibcite{tj433}{11}
+\bibcite{np120}{12}
Modified: pkg/inst/doc/adegenet-basics.log
===================================================================
--- pkg/inst/doc/adegenet-basics.log 2011-06-16 16:11:07 UTC (rev 916)
+++ pkg/inst/doc/adegenet-basics.log 2011-06-16 16:56:36 UTC (rev 917)
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2011.4.12) 16 JUN 2011 17:04
+This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2011.4.12) 16 JUN 2011 17:44
entering extended mode
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**adegenet-basics.tex
@@ -671,13 +671,6 @@
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Here is how much of TeX's memory you used:
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- 9076 multiletter control sequences out of 15000+50000
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38i,6n,36p,282b,495s stack positions out of 5000i,500n,10000p,200000b,50000s
@@ -1081,9 +1053,9 @@
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/adegenet -r 917
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