Hi Alejandro, I fixed the bug in devel branch, may be updated one day later, please try again to see if that fix works for you. I recently changed Txdb plot, and other features, actually don't have time to update vignettes accordingly yet, please let me know if you have further problem, I will try my best to fix it asap. Thanks Tengfei On Fri, Oct 18, 2013 at 1:05 PM, Tengfei Yin wrote: > Hi Alejandro, > > Thanks for reporting, I believe that's a bug caused by my recent > modification in biovizBase package, I am working on that now, will keep you > updated. > > Best > > Tengfei > > > On Fri, Oct 18, 2013 at 12:43 PM, Alejandro Reyes > wrote: > >> Dear Tengfei Yin, >> >> Firstly, thanks for developing ggbio, it has been very useful for me! >> >> I am getting an error when using autoplot with some specific genomic >> regions in transcriptDb objects, here is an example: >> >> > suppressMessages( library(ggbio) ) >> > suppressMessages(library(**GenomicFeatures)) >> > tx <- makeTranscriptDbFromBiomart() >> >> Aggregating TranscriptDb... >> Parsing exons... >> Parsing cds... >> Parsing transcripts... >> Parsing utrs and aggregating... >> Done >> Constructing graphics... >> >> prueba <- GRanges( 16, IRanges( start=69598997, 69718569 ) ) >> autoplot( tx, prueba, group.selfish=TRUE, names.expr="") >> >> Aggregating TranscriptDb... >> Parsing exons... >> Parsing cds... >> Parsing transcripts... >> Parsing utrs and aggregating... >> Done >> Constructing graphics... >> >> So far, excellent, however, when I look into a smaller region I get an >> error message: >> >> > prueba <- GRanges( "16", IRanges(start=69718724, end=69720078 )) >> > autoplot( tx, prueba, group.selfish=TRUE, names.expr="") >> Aggregating TranscriptDb... >> Parsing exons... >> Parsing cds... >> Parsing transcripts... >> Parsing utrs and aggregating... >> Error in DataFrame(...) : different row counts implied by arguments >> >> I believe it has to do with recent modifications of ggbio, since I do not >> get the error message with older versions, e.g. 1.9.7. >> >> > sessionInfo() >> R Under development (unstable) (2013-07-01 r63121) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] ggbio_1.11.0 ggplot2_0.9.3.1 GenomicFeatures_1.15.0 >> [4] AnnotationDbi_1.23.28 Biobase_2.21.7 GenomicRanges_1.13.56 >> [7] XVector_0.1.4 IRanges_1.19.40 BiocGenerics_0.7.8 >> [10] BiocInstaller_1.13.1 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.17.3 Biostrings_2.29.19 biovizBase_1.9.4 >> [4] bitops_1.0-6 BSgenome_1.29.1 cluster_1.14.4 >> [7] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >> [10] digest_0.6.3 grid_3.1.0 gridExtra_0.9.1 >> [13] gtable_0.1.2 Hmisc_3.12-2 labeling_0.2 >> [16] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >> [19] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 >> [22] RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >> [25] Rsamtools_1.13.53 RSQLite_0.11.4 rtracklayer_1.21.14 >> [28] scales_0.2.3 stats4_3.1.0 stringr_0.6.2 >> [31] tools_3.1.0 VariantAnnotation_1.7.57 XML_3.98-1.1 >> [34] zlibbioc_1.7.0 >> >> Best regards, >> Alejandro Reyes >> > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]