R/plotIBD.R

In Liubuntu/SeqSQC: A bioconductor package for sample quality check with next generation sequencing data

plotIBD <- function(res.qc, interactive = FALSE){

    centers <- data.frame(k0=c(0, 0, 0.25, 0.5, 1),
                          k1=c(0, 1, 0.5, 0.5, 0),
                          label=factor(c("DU", "PO", "FS", "HF", "UN"))
                          )
    prob.ind <- as.character(res.qc$relation) == "UN" &
        as.character(res.qc$pred.label) == "Related"
    prob.ibd <- res.qc[prob.ind, ]

    p <- ggplot(data=res.qc, aes(x=k0, y=k1))
    p <- p + geom_point(aes(shape=type, colour=relation))
    p <- p + scale_colour_discrete(drop = FALSE)
    p <- p + geom_point(aes(colour=label), shape=3, data=centers)
    cols <- c(brewer.pal(n=9, name="Set1")[c(1,3,5,8)], "black")
    p <- p + scale_color_manual(values=cols)
    if(nrow(prob.ibd) > 0){
        p <- p + geom_point(data=prob.ibd, aes(x=k0, y=k1),
                            shape=1, colour="red", size=4)
    }
    p <- p + theme_classic()
    p <- p + theme(legend.position = c(0.9, 0.8))
    p <- p + labs(x="K0 (probability that two individuals share 0 alleles)",
                  y="K1 (probability that two individuals share 1 alleles)",
                  col="Relation",
                  shape="Type")

    if(interactive){
        return(ggplotly(p))
    }else{
        return(p)
    }
}