I'm wondering whether there are simple tools (e.g. Java, R/Bioconductor) available for plotting positions of custom SNPs on top of gene region (exons and introns). I don't have p-values for these SNPs and LD map is not of my interest - I'm aware of SNAP, SNIPA, LocusZoom etc, but all I want is a simple plot with genomic region, gene structure (exons and introns) and SNPs that fall into that region. Isoforms are optional.
Did you ever figure out a good package to do this? I am trying to do the same thing! I have been looking at bioconductor's ggbio but haven't figured out an easy way to do what I want, which is to plot SNP effect sizes above gene regions and visually show where these SNPs occur in the gene. Any help would be appreciated!
Try the needle plot from intogen.org , or if you have your own bunch of snps in a vcf file and then find out if there is a driver you can see this kind of plots for the driver genes that come from your data vcf based on the analysis plots or if you want directly for yourself then use the package here . You can also see the tool CRAVAT which does something similar plots of input variants and already annotated variants post annotation with the tool.
