Hi Rebecca, So sorry for the late reply, in case I forget next time, please feel free to leave your question/feedback in github issues page backlog <https: github.com="" tengfei="" ggbio="" issues="">. I will work on those issues when I got time. For you question, yes, I just confirmed this is a bug in biovizBase/ggbio package for exons with no cds, I fixed the released branch biovizBase(1.12.2) and ggbio(1.12.9) (will fix the devel branch later this week), please update your packages two days later to see if my fix solved the problem or not. thanks again for reporting the bug! cheers On Tue, Jul 8, 2014 at 1:55 PM, sun <fireflysrb at="" gmail.com=""> wrote: > Hello, > > I tried to draw the gene model by using autoplot() in ggbio package with > the following codes. > > library(ggbio) > library("TxDb.Hsapiens.UCSC.hg19.knownGene") > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > data(genesymbol, package = "biovizBase") > autoplot(txdb,which = genesymbol["ACSS2"],names.expr ="tx_name") > > There is only one straight line and no any exons displayed for > "uc010zum.1", which actually has 6 exons. Anything wrong? > > exons <- exonsBy(txdb, "tx",use.names=TRUE) > exons[which(names(exons)=="uc010zum.1")] > GRangesList of length 1: > $uc010zum.1 > GRanges with 6 ranges and 3 metadata columns: > seqnames ranges strand | exon_id exon_name > exon_rank > <rle> <iranges> <rle> | <integer> <character> > <integer> > [1] chr20 [33464328, 33464626] + | 252380 <na> > 1 > [2] chr20 [33470597, 33470792] + | 252381 <na> > 2 > [3] chr20 [33511126, 33511234] + | 252394 <na> > 3 > [4] chr20 [33513501, 33513569] + | 252395 <na> > 4 > [5] chr20 [33513908, 33514084] + | 252396 <na> > 5 > [6] chr20 [33514680, 33514754] + | 252397 <na> > 6 > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] XVector_0.4.0 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > GenomicFeatures_1.16.2 > [4] AnnotationDbi_1.26.0 > Biobase_2.24.0 > GenomicRanges_1.16.3 > [7] GenomeInfoDb_1.0.2 > IRanges_1.22.9 > ggbio_1.12.8 > [10] ggplot2_1.0.0 > BiocGenerics_0.10.0 > > Thanks, > > Rebecca > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tengfei Yin, PhD Product Manager Seven Bridges Genomics sbgenomics.com One Broadway FL 7 Cambridge, MA 02142 (617) 866-0446 [[alternative HTML version deleted]]