I'm trying to make a lollipop chart to show variants on a gene of interest. I have gotten so far as plotting them along the coding regions, and coloring the features of the gene, but I am having trouble coloring the lollipops to indicate the type of mutation (missense, synonymous, etc.). I made a new column called "snpEff_ann_colors" in my data.frame that lists the color and associates it with the type of mutation:

> Gene_exonic_SNPs$snpEff_ann_colors

[1] aquamarine       azure            darkseagreen1    darkseagreen1    azure           
  [6] azure            darkseagreen1    azure            azure            darkseagreen1   
 [11] azure            azure            darkseagreen1    darkseagreen1    darkseagreen1

I then did:

gene.gr$color <- Gene_exonic_SNPs$snpEff_ann_colors

When I plotted, the colors were not correct:

lolliplotgene.gr, domains, ranges = GRanges("chrX", IRanges(1, 239)))

I noticed that they did this differently in TrackViewer documentation:

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

When I did the same in my console, when I print sample.gr$color, it is a list of numbers... However, I would like to have mine be the list that I give it... is there a way to do this?