Highlighting Significantly Associated Sites on Manhattan Plot using ggbio
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graggsd • 0
@graggsd-11168
Last seen 5.6 years ago

Hi all,

I'm experiencing difficulty implementing the highlight.gr argument within the plotGrandlinear function of ggbio. I'm trying to highlight and label significant sites from an association study. I can produce a manhattan plot, but cannot seem to get my significant points highlighted and labeled. Sample code here:

highlight_gr <- gr[which(p.adjust(alt_fit$p.value[,3],
    method = "bonferroni") < 0.05),]
mcols(gr) <- -log10(alt_fit$p.value)

plotGrandLinear(gr,
    aes(y = dxMM),
    color = c("#7fc97f", "#fdc086"),
    cutoff = -log10(0.05 / length(gr)),
    cutoff.color = "black",
    hightlight.gr = highlight_gr,
    highlight.label = TRUE,
    highlight.col = "red") +
    theme(axis.text.x=element_text(angle=-90, hjust=0))
ggbio manhattan plot plotGrandLinear • 648 views
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