On the Trackviewer documentation: https://www.bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html#lolliplot They have a way of specifying colors of mutations along a gene using Lolliplot:

sample.gr$color <- sample.int(6, length(SNP), replace=TRUE)
lolliplotsample.gr, features)

I want to specify colors using a list of colors that I made to associate a specific color with the type of mutation. I don't understand how sample.int is specifying colors, or how to make it so that my colors are the ones being shown.