Thank you for fixing this Tengfei! Just tested it on biovizBase 1.10.4 And I understand that ggbio is still being developed (which is great!) so things might break here and there. If I find anything, I'll let you know as usual =) Cheers, Leo On Fri, Nov 22, 2013 at 11:23 AM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > just fixed in biovizBase 1.10.4 (bioc 2.13), biovizBase 1.11.4 (bioc 2.14 > devel) > > Thanks, please let me know if you have further issues/problem. > > Tengfei > > > On Fri, Nov 22, 2013 at 10:57 AM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > >> Hi again Leonardo :) >> >> I apologize for the inconvenience, frankly speaking, this version of >> ggbio/biovizBase is still more like devel version though it's already in >> release, but on the other hand, I can get lots of great feedback and fix >> them as fast as I could. Anyway, I found the bug and will fix them soon >> today. >> >> Thanks >> >> Tengfei >> >> >> On Fri, Nov 22, 2013 at 1:29 AM, Leonardo Collado Torres < >> lcollado@jhsph.edu> wrote: >> >>> Hello again Tengfei and BioC list, >>> >>> I am encountering a new error when using autoplot() on a GRanges and an >>> annotation data base. >>> >>> I suspect that there is no annotation on the region I selected. For now >>> I believe I can use a tryCatch() to pick up the error and avoid plotting >>> this track on situations like this. But well, it would be nice if ggbio >>> handled this error or maybe the cause it something else. >>> >>> >>> >>> > suppressMessages(library("ggbio")) >>> > suppressMessages(library("GenomicRanges")) >>> > suppressMessages(library("TxDb.Hsapiens.UCSC.hg19.knownGene")) >>> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >>> > wh <- GRanges("chr21", IRanges(47409355, 47409855)) >>> > autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") >>> Aggregating TranscriptDb... >>> Parsing exons... >>> Parsing cds... >>> Parsing transcripts... >>> Parsing utrs and aggregating... >>> Error in DataFrame(...) : different row counts implied by arguments >>> > traceback() >>> 14: stop("different row counts implied by arguments") >>> 13: DataFrame(...) >>> 12: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = >>> strand, >>> mcols = DataFrame(...), seqlengths = seqlengths, seqinfo = >>> seqinfo) >>> 11: GRanges(seqnms, ir.utrs, tx_id = .nms, tx_name = .tx.nms, gene_id = >>> .gid.nms, >>> type = "utr") >>> 10: .local(obj, ...) >>> 9: crunch(object, which, truncate.gaps = truncate.gaps, truncate.fun = >>> truncate.fun, >>> ratio = ratio) >>> 8: crunch(object, which, truncate.gaps = truncate.gaps, truncate.fun = >>> truncate.fun, >>> ratio = ratio) >>> 7: .local(data, ...) >>> 6: (function (data, ...) >>> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="">>> "TranscriptDb">, >>> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >>> stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE, >>> which = <s4 object="" of="" class="" "granges"="">, list()) >>> 5: (function (data, ...) >>> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="">>> "TranscriptDb">, >>> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >>> stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE, >>> which = <s4 object="" of="" class="" "granges"="">, list()) >>> 4: do.call(geom_alignment, args.res) >>> 3: .local(object, ...) >>> 2: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") >>> 1: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") >>> > sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> 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] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.14.2 >>> AnnotationDbi_1.24.0 >>> [4] Biobase_2.22.0 GenomicRanges_1.14.3 >>> XVector_0.2.0 >>> [7] IRanges_1.20.5 BiocGenerics_0.8.0 >>> ggbio_1.10.8 >>> [10] ggplot2_0.9.3.1 >>> >>> loaded via a namespace (and not attached): >>> [1] biomaRt_2.18.0 Biostrings_2.30.1 biovizBase_1.10.3 >>> bitops_1.0-6 BSgenome_1.30.0 >>> [6] cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 >>> dichromat_2.0-0 digest_0.6.3 >>> [11] grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 >>> Hmisc_3.12-2 labeling_0.2 >>> [16] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>> plyr_1.8 proto_0.3-10 >>> [21] RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 >>> rpart_4.1-3 Rsamtools_1.14.1 >>> [26] RSQLite_0.11.4 rtracklayer_1.22.0 scales_0.2.3 >>> stats4_3.0.2 stringr_0.6.2 >>> [31] tools_3.0.2 VariantAnnotation_1.8.6 XML_3.95-0.2 >>> zlibbioc_1.8.0 >>> > >>> >>> >>> Thank you! >>> >>> Leonardo Collado Torres, PhD student >>> Department of Biostatistics >>> Johns Hopkins University >>> Bloomberg School of Public Health >>> Website: http://www.biostat.jhsph.edu/~lcollado/<http: bit.ly="" lcolladotorres=""> >>> Blog: http://lcolladotor.github.io/ <http: bit.ly="" fellbit=""> >>> >>> >>> >>> >> >> >> -- >> 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]]