R/plotMissingRate.R

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

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

    res.pop.ord <- res.qc
    res.pop.ord$outlier <- ifelse(res.pop.ord$missingRate > 0.1, "Yes", "No")
    res.pop.ord$problematic <- factor(res.pop.ord$outlier, levels=c("Yes", "No"))
    
    if(interactive){
        p1 <- suppressWarnings(figure(ylim=c(-0.1, 1))) %>%
            ly_points(
                missingRate, data=res.pop.ord, color = problematic, glyph = type,
                hover=list(sample, missingRate)
            ) %>%
            ly_abline(h=0.1, type=2)
        return(p1)
    }else{
        p <- ggplot(data=res.pop.ord, aes(x=sample, y=missingRate))
        p <- p + geom_point(aes(colour=problematic, shape=type))
        p <- p + scale_color_discrete(drop = FALSE)
        p <- p + geom_hline(yintercept=0.1, colour="grey")
        p <- p + theme(axis.text.x=element_blank())
        return(p)
    }
}