Com a legenda, fica:
Nomes <- c("PentaE","D18S51","D21S11","TH01","D3S1358","FGA")
NAgel <- c(0.14970140,0.06891474,0.13054984,0.26187191,0.06763797,0.08232084)
NAcap <- c(0.09954859,0.05968163,0.11116655,0.07833215,0.05561891,0.08612497)
Matriz <- matrix(c(NAgel,NAcap),,2)
library(plotrix)
Matriz<-matrix(c(NAgel,NAcap),ncol=6,by=T)
barpos<-barp(Matriz,main="Gráfico de Barras",col=1:2,
names.arg=c(Nomes),cex=0.8,cylindrical=TRUE,shadow=TRUE,
xlab="Grupos",ylab="Resposta",legend.lab=c("NAgel","NAcap"),
legend.pos=list(x=1.2,y=0.248))
Att.
André