I wish to plot a transcript with the UTRs as thinner boxes. BiomartGeneRegionTrack does this automatically:

transcriptID <- "ENST00000398958"

# ---------- USING MART

mart <- biomaRt::useMart(
  biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_ensembl",
  host = "dec2013.archive.ensembl.org")

# Create transcript track
biomartTrack <- Gviz::BiomartGeneRegionTrack(
  filters = list(
    ensembl_transcript_id = transcriptID),
  biomart = mart)

# Plots with UTRs as thinner boxes
Gviz::plotTracks(biomartTrack)

But as I cannot connect to the internet for each plot I create, I need to use a TxDb from a local file:

transcriptID <- "ENST00000398958"

# ---------- USING TXDB

txdbhg19 <- AnnotationDbi::loadDb(file = "Biomart_Ensembl_HS_dec2013.archive.ensembl.org.sqlite")

# The sqlite was created like this:
# txdbhg19 <- GenomicFeatures::makeTxDbFromBiomart(
#   biomart = "ENSEMBL_MART_ENSEMBL",
#   dataset = "hsapiens_gene_ensembl",
#   host = "dec2013.archive.ensembl.org")
# AnnotationDbi::saveDb(txdbhg19, file="Biomart_Ensembl_HS_dec2013.archive.ensembl.org.sqlite")

# See what data can be retrieved
columns(txdbhg19)
# [1] "CDSCHROM"   "CDSEND"     "CDSID"      "CDSNAME"    "CDSSTART"   "CDSSTRAND"  "EXONCHROM"  "EXONEND"    "EXONID"     "EXONNAME"
# [11] "EXONRANK"   "EXONSTART"  "EXONSTRAND" "GENEID"     "TXCHROM"    "TXEND"      "TXID"       "TXNAME"     "TXSTART"    "TXSTRAND"
# [21] "TXTYPE"

# Which of these columns will help me?

# Get all exon information
allExons <- GenomicFeatures::exons(
  txdbhg19,
  filter = list(tx_name = transcriptID),
  columns = list())

# I wish to create a GeneRegionTrack that has the same feature values as the BiomartGeneRegionTrack above has:
Gviz::feature(biomartTrack)
# [1] "utr5"           "utr5"           "utr5"           "utr5"           "protein_coding" "protein_coding" "protein_coding"
# [8] "protein_coding" "protein_coding" "protein_coding" "protein_coding" "protein_coding" "protein_coding" "utr3"

# But I'm not sure how to accomplish this.

Can anyone help me create the same plot using the TxDb?

Last I thought Gviz took care of this already (and I think I actually helped provide a patch for that several years back now :-) -- does it no longer work?

Look at page 42 of the current Gviz vignette where the plot from plotTracks(txTr) is shown ... looks about right to me, no?

Did you check the section in the vignette that Steve was referring to? You can build a GeneRegionTrack straight from a TxDB object, and that will give you all the UTRs just as you get them from Biomart:

library(GenomicFeatures)
options(ucscChromosomeNames=FALSE)
grt <- GeneRegionTrack(txdbhg19)
plotTracks(grt, from=1e6, to=2e6)

Btw, I'd recommend to not calling functions from their Namespace with the :: notation, unless there is a good reason to do so. You should always properly attach the packages you need using library() calls. Otherwise there is no guarantee that all dependencies in the search path are properly resolved.

Florian