plotRECON legend specs

[HedvigS]

Is there a way of removing the legend in plotRECON, or explicitly paste what they should be? By default, I get it as "1, R1" and since they're both in the same rate category I'd prefer to either set the labels myself (e.g. just "1"), or remove the legend altogether.

[jamie-thompson]

Is it possible to move the legend?

[jcoliver]

As of now, plotRECON() is fairly hard-coded and does not allow moving the legend. However, the function itself is fairly short, so you could, instead of calling plotRECON(), replicate the code that function uses and modify legend through the call to legend().

The plotRECON() function (also available in the R folder):

plotRECON <- function(phy, likelihoods, piecolors=NULL, cex=0.5, pie.cex=0.25, file=NULL, height=11, width=8.5, show.tip.label=TRUE, title=NULL, ...){
    if(is.null(piecolors)){
        piecolors=c("white","black","red","yellow","forestgreen","blue","coral","aquamarine","darkorchid","gold","grey","yellow","#3288BD","#E31A1C")
    }
    if(!is.null(file)){
        pdf(file, height=height, width=width,useDingbats=FALSE)
    }
    plot(phy, cex=cex, show.tip.label=show.tip.label, ...)

    if(!is.null(title)){
        title(main=title)
    }
    nodelabels(pie=likelihoods,piecol=piecolors, cex=pie.cex)
    states <- colnames(likelihoods)
    legend(x="topleft", states, cex=0.8, pt.bg=piecolors,col="black",pch=21);

    if(!is.null(file)){
        dev.off()
    }
}

A short bit of code that does what the function does, but putting legend in bottom right (you'll need to make sure the required objects (phy, likelihoods, states) exist (or change the names to match your data)):

piecolors=c("white","black","red","yellow","forestgreen","blue","coral","aquamarine","darkorchid","gold","grey","yellow","#3288BD","#E31A1C")
plot(phy)
nodelabels(pie=likelihoods,piecol=piecolors)
states <- colnames(likelihoods)
legend(x="bottomright", states);