Nothing
plot_ranks <- function(ranks, plot.CIs=FALSE, ordered.by.rank=TRUE,identities=NULL,plot.identities=TRUE,colors=NULL) {
ranks <- apply(ranks,2,function(x) { rank(-x) })
if (is.null(identities)) {
identities <- rownames(ranks)
}
if (dim(ranks)[2] > 1) {
mean.ranks <- rowMeans(ranks)
} else {
mean.ranks <- ranks
}
if (is.null(colors)) {
colors <- rep("black",length(identities))
}
if (ordered.by.rank==TRUE) {
colors <- colors[order(mean.ranks)]
identities <- identities[order(mean.ranks)]
if (plot.CIs==TRUE) {
CIs <- apply(ranks,1,quantile,c(0.025,0.975),na.rm=TRUE)
CIs <- CIs[,order(mean.ranks)]
}
mean.ranks <- mean.ranks[order(mean.ranks)]
} else {
if (plot.CIs==TRUE) {
CIs <- apply(ranks,1,quantile,c(0.025,0.975),na.rm=TRUE)
}
}
x <- 1:length(identities)
if (plot.identities==TRUE) {
plot(x, mean.ranks,pch=20,cex=1.5,axes=FALSE,xlab="Identity",ylab="Dominance rank",col=colors,ylim=c(max(ranks,na.rm=T),min(ranks,na.rm=T)))
axis(2)
axis(1,at=x,labels=identities,las=3)
box()
} else {
plot(x,mean.ranks,pch=20,cex=1.5,xlab="Identity",ylab="Dominance rank",col=colors,ylim=c(max(ranks,na.rm=T),1))
}
if (plot.CIs==TRUE) {
arrows(x,CIs[1,],x,CIs[2,],code=3,angle=90,length=0.1,col=colors)
}
}
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