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stianlagstad / chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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Investigate 5' and 3' marker error in fusionPlot #9

Open stianlagstad opened 6 years ago

stianlagstad commented 6 years ago

The 5' and 3' markers on the fusion plot seems to be off. See the plot here.

stianlagstad commented 6 years ago

Possibly a Gviz bug. This code:

transcriptID <- "ENST00000395443"

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)

# Create axis track
axisTrack <- Gviz::GenomeAxisTrack()
displayPars(axisTrack) <- list(
  add53 = TRUE,
  labelPos = "below",
  cex = 1.5
)

Gviz::plotTracks(
  c(biomartTrack, axisTrack),
  chromosome = "chr3",
  add53 = TRUE,
  add35 = TRUE)

Produces this: rplot

I've posted a question on the Bioconductor support site.