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!