R/plotSexCheck.R

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

plotSexCheck <- function(res.qc, interactive=FALSE){
    if (any(res.qc$sex == "")) {
        warning("Please provide sex info for all study samples!")
        res.qc <- res.qc[res.qc$sex != "", ]
    }
    res.pop.ord <- res.qc
    prob.ind <- res.pop.ord$sex == "female" & res.pop.ord$pred.sex == "male" |
        res.pop.ord$sex == "male" & res.pop.ord$pred.sex == "female"
    prob.sex <- res.pop.ord[prob.ind, ]
    
    p <- ggplot(data=res.pop.ord, aes(x=sample, y=sexinb))
    p <- p + geom_point(aes(colour=sex, shape=type))
    p <- p + scale_colour_discrete(drop = FALSE)
    p <- p + labs(col="Self-reported gender",
                  shape="Type",
                  x="Sample",
                  y="Sex inbreeding coefficient")
    p <- p + geom_hline(yintercept=c(0.2, 0.8), colour="grey")
    if(nrow(prob.sex) > 0){
        p <- p + geom_point(data=prob.sex,
                            aes(x=sample, y=sexinb), shape=1,
                            colour="red", size=4)
    }
    p <- p + theme_classic()
    p <- p + theme(axis.text.x=element_blank(),
                   axis.ticks.x=element_blank())  
    ## p <- p + theme(legend.position = c(0.2, 0.5))
    if(interactive){
        return(ggplotly(p))
    }else{
        return(p)
    }
}