I am using gviz from a bioconductor to plot SNPs data using chromosome and genome axis:
My problem is that it plots dense located SNPs under each other and I could not find a parameter to avoid. I also could not find if it is possible to plot the name of the SNPs to the corresponding bar or mark one specific SNP with another color.
gr99 <- GRanges(seqnames = c("chr7","chr7","chr7","chr7","chr7","chr7"),
atrack2=AnnotationTrack(gr99, name = "SNP")
gen = c()
gtrack <- GenomeAxisTrack()
itrack <- IdeogramTrack(genome = gen, chromosome = "chr7")
plotTracks(list(itrack,gtrack, atrack2),panel.only == TRUE)