Hi Alejandro, Would you mind send me a picture of that (off mailing list is ok), do you just see a utr and exons? I want to make sure how it looks like, there are two possible reason for that 1. you pass xlim in autoplot, it will cut the data 2. I think you just want to zoom into the region to check details, and keep introns and everyting, you probably need to generate a larger region and use +xlim(granges) to zoom in without cutting any data. I am not sure is that due to the above reason or new bugs, so the picture will help. Thanks Tengfei On Tue, Oct 22, 2013 at 4:12 AM, Alejandro Reyes <alejandro.reyes@embl.de>wrote: > Hi Tengfei, > > Thanks for the fix! It does not give an error anymore, however, in the > case below, the lines representing the introns (e.g. ---->---->---->---) > are not being plotted. I am getting a warning as well, see case below: > > > > suppressMessages( library(ggbio) ) > > suppressMessages(library(**GenomicFeatures)) > > tx <- makeTranscriptDbFromBiomart() > Download and preprocess the 'transcripts' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... OK > Download and preprocess the 'splicings' data frame ... OK > Download and preprocess the 'genes' data frame ... OK > Prepare the 'metadata' data frame ... OK > Make the TranscriptDb object ... OK > > > > This works great: > > > > > > 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... > > > > This does not draw the introns and produces a warning: > > > > > > 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... > Done > Constructing graphics... > Warning message: > In ans[] <- x : > number of items to replace is not a multiple of replacement length > > > sessionInfo() > > R Under development (unstable) (2013-10-21 r64088) > > 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] GenomicFeatures_1.15.0 AnnotationDbi_1.25.0 Biobase_2.23.1 > [4] GenomicRanges_1.15.1 XVector_0.3.0 IRanges_1.21.2 > [7] BiocGenerics_0.9.0 ggbio_1.11.1 ggplot2_0.9.3.1 > > [10] BiocInstaller_1.13.1 > > loaded via a namespace (and not attached): > [1] biomaRt_2.19.0 Biostrings_2.31.0 biovizBase_1.11.1 > [4] bitops_1.0-6 BSgenome_1.31.0 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_1.15.2 RSQLite_0.11.4 rtracklayer_1.23.1 > [28] scales_0.2.3 stats4_3.1.0 stringr_0.6.2 > [31] tools_3.1.0 VariantAnnotation_1.9.3 XML_3.98-1.1 > [34] zlibbioc_1.9.0 > > > Thanks again and let me know if you need additional information! > > Alejandro > > > > 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 <tengfei.yin@sbgenomics.com<mailto:>> tengfei.yin@**sbgenomics.com <tengfei.yin@sbgenomics.com>>> 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 >> <alejandro.reyes@embl.de <mailto:alejandro.reyes@embl.**de<alejandro.reyes@embl.de="">>> >> 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 <http: sbgenomics.com=""/> >> >> 625 Mt. Auburn St. Suite #208 >> Cambridge, MA 02138 >> (617) 866-0446 >> >> >> >> >> -- >> Tengfei Yin, PhD >> Seven Bridges Genomics >> sbgenomics.com <http: 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]]