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Add optional label parameters to the evolution functions, to support translating plots to other languages. #1

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Add optional label parameters to the evolution functions, to support translating plots to other languages. #1

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18 changes: 15 additions & 3 deletions R/evolution.R
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Original file line number Diff line number Diff line change
Expand Up @@ -304,6 +304,10 @@ plot.coalescent.plot<-function(x,...){
drift.selection<-function(p0=0.5,Ne=100,w=c(1,1,1),ngen=400,nrep=10,
colors=NULL,...){
if(is.null(colors)) colors<-rainbow(nrep)
if(hasArg(xlabel)) xlabel=list(...)$xlabel
else xlabel<-"Time (generations)"
if(hasArg(ylabel)) ylabel=list(...)$ylabel
else ylabel<-"f(A)"
w<-(w/max(w))[3:1]
gametes<-rep(0,2*Ne)
if(p0>0) gametes[1:round(p0*2*Ne)]<-1
Expand All @@ -324,7 +328,7 @@ drift.selection<-function(p0=0.5,Ne=100,w=c(1,1,1),ngen=400,nrep=10,
for(j in 1:nrep) p[[j]][i+1]<-mean(gametes[[j]])
}
plot(0:ngen,p[[1]],type="l",col=colors[1],lwd=2,ylim=c(0,1),
xlab="time (generations)",ylab="f(A)")
xlab=xlabel,ylab=ylabel)
if(nrep>1)
nulo<-mapply(lines,x=replicate(nrep-1,0:ngen,simplify=FALSE),
y=p[2:nrep],col=colors[2:nrep],lwd=2)
Expand Down Expand Up @@ -356,8 +360,12 @@ plot.drift.selection<-function(x,...){
else type<-"l"
if(hasArg(lwd)) lwd<-list(...)$lwd
else lwd<-2
if(hasArg(xlabel)) xlabel=list(...)$xlabel
else xlabel<-"Time (generations)"
if(hasArg(ylabel)) ylabel=list(...)$ylabel
else ylabel<-"f(A)"
plot(0:ngen,x[[1]],type=type,col=colors[1],lwd=lwd,ylim=c(0,1),
xlab="time (generations)",ylab="f(A)")
xlab=xlabel,ylab=ylabel)
if(nrep>1)
nulo<-mapply(lines,x=replicate(nrep-1,0:ngen,simplify=FALSE),
y=x[2:nrep],col=colors[2:nrep],type=type,lwd=lwd)
Expand All @@ -370,6 +378,10 @@ msd<-function(p0=c(0.5,0.5),Ne=c(100,100),
colors=c("red","blue"),...){
if(hasArg(show.legend)) show.legend=list(...)$show.legend
else show.legend<-TRUE
if(hasArg(xlabel)) xlabel=list(...)$xlabel
else xlabel<-"Time (generations)"
if(hasArg(ylabel)) ylabel=list(...)$ylabel
else ylabel<-"f(A)"
w<-lapply(w,function(w) (w/max(w))[3:1])
gametes<-lapply(Ne,function(Ne) rep(0,2*Ne))
gametes<-mapply(function(p0,g,N){
Expand Down Expand Up @@ -404,7 +416,7 @@ msd<-function(p0=c(0.5,0.5),Ne=c(100,100),
for(j in 1:2) p[[j]][i+1]<-mean(gametes[[j]])
}
plot(0:ngen,p[[1]],type="l",col=colors[1],lwd=2,ylim=c(0,1),
xlab="time (generations)",ylab="f(A)")
xlab=xlabel,ylab=ylabel)
lines(x=0:ngen,y=p[[2]],col=colors[2],lwd=2)
if(show.legend) legend(x="topright",legend=1:2,lty=1,col=colors,
lwd=2,bg=make.transparent("white",0.8))
Expand Down
2 changes: 1 addition & 1 deletion man/drift.selection.Rd
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Expand Up @@ -11,7 +11,7 @@
\item{nrep}{number of replicate simulations.}
\item{ngen}{total time, in number of generations, for the simulation.}
\item{colors}{colors to use for plotting.}
\item{...}{optional arguments. Presently the only arguments are \code{type} (e.g., \code{"l"}, \code{"s"}) and \code{lwd} in the \code{plot} method.}
\item{...}{optional arguments. Presently the only arguments are \code{type} (e.g., \code{"l"}, \code{"s"}) and \code{lwd} in the \code{plot} method. \code{xlabel} and \code{ylabel} sets the labels for the x and y axes, respectively.)}
}
\description{
Simulates drift and natural selection at a single biallelic locus within one or various populations.
Expand Down
2 changes: 1 addition & 1 deletion man/genetic.drift.Rd
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Expand Up @@ -11,7 +11,7 @@
\item{time}{Total time, in number of generations, for the simulation.}
\item{show}{Various options for plotting. \code{"p"} shows the frequency of the A allele through time; \code{"genotypes"} creates an animated histogram with the frequencies of each of the three genotypes through time; \code{"fixed"} shows the fraction of populations that have fixed for each allele, a or A; \code{"heterozygosity"} plots the mean heterozygosity and the expected heterozygosity through time. The default is \code{show="p"}.}
\item{pause}{Pause between generations. \code{pause=0.01} (for instance) might smooth animation.}
\item{...}{optional arguments. In \code{genetic.drift} the optional arguments are presently: \code{colors} (a vector giving the colors to be used to graph the various simulations); and \code{lwd}. The \code{plot} method of the object class adds the optional argument \code{type} (e.g., \code{"l"} or \code{"s"}.)}
\item{...}{optional arguments. In \code{genetic.drift} the optional arguments are presently: \code{colors} (a vector giving the colors to be used to graph the various simulations); and \code{lwd}. The \code{plot} method of the object class adds the optional argument \code{type} (e.g., \code{"l"} or \code{"s"}. \code{xlabel} and \code{ylabel} sets the labels for the x and y axes, respectively.)}
}
\description{
This function simulates genetic drift at a biallelic genetic locus with no selection and no mutation in a sexually reproducing diploid population or set of populations. It is essentially redundant with \code{\link{drift.selection}}, but in which there is no difference in relative fitness among genotypes; however, it also allows the user to visualize heterozygosity or genetic variation through time - options that are not yet implemented in \code{\link{drift.selection}}.
Expand Down