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Plotting Fst

Hello,

I have a huge SNP dataset of 25 millions SNP genome wide. I have divided it into different chromosomes and this FST plot is for chromosome 1. To generate this plot and for it to be visually tractable, I have chosen SNPs every 50 bp. But the plot is still not very good and there are many many SNPs with the same overall FST value. I was wondering is there any way to reduce the noise in this plot, kind of taking down most points, something like logarithm. Any help is very much appreciated.

Thanks a lot in advance.enter image description here

fst
• 6,396 views • link
updated by Biostar Biostar • written by thjnant thjnant

Seems like you are using ggplot to plot these, did you try to use jitter and add alpha value to your dots, so they will be semi-transparent?

• 0 views • link
written by Pavel Senin Pavel Senin

1 answer

Here, I think that jitter helps with that line of constant values

require(ggplot2)
require(Cairo)
require(grid)
data = data.frame(x=c(runif(15000)*1e+08,runif(450)*1e+08),
                  y=c(runif(15000),rep(0.3,450)))
p <- ggplot(data, aes(x, y)) 
p1 <- p + geom_point(cex=0.9)
p2 <- p + geom_jitter(position = position_jitter(w = 0.01, h = 0.02), 
                      colour="darkorchid3", alpha=0.3,cex=0.9)
Cairo(width = 800, height = 400, file="test.png")
print(grid.arrange(p1, p2, ncol=2))
dev.off()

enter image description here

• 611 views • link
written by Pavel Senin Pavel Senin

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