I would recommend using a tool specific for plotting data on the genome such as karyoploteR. With this kind of tools, you'll get all your chromosomes into scale for free.
The code would be something like this (untested):
comment.char = "#")
#make a GRanges with your data (we need to repeat column 2 as start and end for this to work)
snps.gr <- toGRanges(snps[,c(1,2,2)])
kp <- plotKaryotype(genome="hg19") #<- use the genome you need, if not human
kp <- kpPlotDensity(kp, data=snps.gr, col="blue")
#To add the axis, first get the max density value
max.density <- kp$latest.plot$computed.values$max.density
kpAxis(kp, ymin=0, ymax=max.density, numticks = 3)
And that's it. With this you should get something like this
You can customize it in many ways (change colors, etc...) or represent only some of the chromosomes or even zoom to specific regions.
You can find more info on that in the karyoploteR tutorial page and specifically in the kpPlotDensity page or the Gene Density example.
Hope this helps