This is more a comment in case anyone else runs into this issue - I'm using Gviz to plot output from RepeatMasker, and the column of TE names is "Target" in the .gff - when plotting with Gviz, the transcriptAnnotation input would just place the text "unknown" with this command:
te_grtrack <- GeneRegionTrack(gff, name="TEs", transcriptAnnotation = "Target")
transcriptAnnotation also seemed unwilling to accept any other column - so I renamed the "Target" column to "symbol", and that worked perfectly. I'm just getting started and I'm not sure exactly why that is, but I figured I would make a note of it - is there something obvious that I am missing that would allow me to plot without changing the column name?
this is what worked:
colnames(gff) <- "symbol"
te_grtrack <- GeneRegionTrack(gff, name="TEs", transcriptAnnotation = "symbol")