I am interested in plotting mutations using the oncoplot function. I want to show the mutational landscape of leukemia patients involved in my research. I have generated .maf files to use with the maftools package, I also have excel files with variant classification data. I classified variants using VarSome according to ACMG classification data. 

My problem is I am not sure which variants should I choose to plot. During my literature review I had a hard time understanding the process which authors selected in plotting their variants. I am not sure should I plot only non-benign somatic mutations, or should I chose more broad approach and plot let's say all mutations that are not present in gnomAD/1000 genomes. 

I just need someone to point me in the right direction.

Thanks in advance :)