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Gene annotations at the edges of the plot can be cut-off. To prevent this, padding can be added at each end of the x-axis using:

mhplot<-manhattan.plot(cleaned$chr, cleaned$pos, cleaned$pvalue, annotate=ann)
mhplot$x.limits<-mhplot$x.limits+10*c(-10,10)
print(mhplot)

Thanks for the code and the tip Matthew :)

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