x-axis is not displaying all my scaffolds in qqman r package
Entering edit mode
3.7 years ago
ggman ▴ 80

Hello friends,

I am using qqman (an R package) to create a manhattan plot from a data set based on statistics. So it is working well but it is omitting 2/3 of my data for whatever reason... I am using this guide to try and solve the issue but I am not sure how to address it. I have 700 scaffolds and it is only showing about 250 scaffolds. When I change the dimensions, it makes the plot cleaner but the x-axis is still omitting my data. I am thinking that if I make the spacing even between the points on the x-axis it would help but it doesn't account for my missing data.

Below is my code from R-studio and the qqman R-package

manhattan(qq.data, chr="chrom", bp = "start", p = "fst", snp = "snp",logp=FALSE,ylab="fst")

Any guidance is appreciated friends!

qqman manhattan plot R package snps R • 1.7k views

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