plot boot.ppfst

[andreiaamaral]

Hello,

is there a function to plot a heatmap with the matrix obtained using boot.ppfst? thanks.

[jgx65]

Hi Andreia, something like this?

plot.boot.ppfst<-function(x,...){
  a<-dim(x$ll)[1]
  ci<-matrix(nrow=a,ncol=a)
  dimnames(ci)<-dimnames(x$ll)
  for (i in 2:a)
    for (j in 1:(a-1)){
      ci[j,i]<-x$ul[j,i]
      ci[i,j]<-x$ll[j,i]
    }
    image(1:a,1:a,ci,xlab="population",ylab="Population")
}

##example use:

data(gtrunchier)
plot(boot.ppfst(gtrunchier[,-2]))

[courtiol]

Indirectly, hierfstat depends both on lattice (via ade4) and ggplot2 (via adegenet): So there would also be the option of declaring a direct dependence to e.g. lattice and coding something with a scale as well. Such as:

plot.boot.ppfst<-function(x,...){
  a<-dim(x$ll)[1]
  ci<-matrix(nrow=a,ncol=a)
  dimnames(ci)<-dimnames(x$ll)
  for (i in 2:a)
    for (j in 1:(a-1)){
      ci[j,i]<-x$ul[j,i]
      ci[i,j]<-x$ll[j,i]
    }
  lattice::levelplot(ci,xlab="Population", ylab="Population", colorkey=list(title="Fst"), ...)
}

data(gtrunchier)
plot(boot.ppfst(gtrunchier[,-2]), col.regions = \(n) rev(grey.colors(n)))

That could open the door for more plotting...

[jgx65]

Thanks for the tip! @andreiaamaral , does this solve your question? I'm closing it now, feel free to reopen if need be

[andreiaamaral]

Hi

sorry thanks for your tips and help!

On Wed, Mar 2, 2022 at 2:22 PM Jerome Goudet @.***> wrote:

Closed #55 https://github.com/jgx65/hierfstat/issues/55.

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