quick update, it's caused by a bug in computing small arrows, current workaround before I check in the fix is to use geom 'segment' or 'chevron' to represent the introns.
autoplot(TxDb.Hsapiens.UCSC.hg19.knownGene, show_region, gap.geom = "segment") Tengfei On Thu, Apr 11, 2013 at 2:36 PM, Tengfei Yin <[email protected]> wrote: > Hi Julian, > > I confirmed the issue, thanks a lot, I will keep you updated on the fix. > > Tengfei > > On Thu, Apr 11, 2013 at 2:05 PM, Julian Gehring <[email protected]> > wrote: >> Hi, >> >> Using the 'autoplot' method for plotting a region of 'TranscriptDb' object >> seems to hang for certain regions, taking up lots of memory and finishing >> only after several minutes: >> >> <code> >> >> library(ggbio) >> library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> library(biovizBase) >> data(genesymbol) >> >> ## this example works fine >> autoplot(TxDb.Hsapiens.UCSC.hg19.knownGene, genesymbol["ALDOA"]) >> >> ## this one not >> show_region = GRanges("chr1", IRanges(3160601, 3160751)) ## contains exons >> and transcripts >> autoplot(TxDb.Hsapiens.UCSC.hg19.knownGene, show_region) >> >> </code> >> >> This seem to affect both the devel as well as the release version. >> >> >> Best wishes >> Julian >> >> >> --- >> R Under development (unstable) (2013-04-10 r62546) >> 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=C 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] biovizBase_1.9.1 >> [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.0 >> [3] GenomicFeatures_1.13.0 >> [4] AnnotationDbi_1.23.1 >> [5] Biobase_2.21.0 >> [6] GenomicRanges_1.13.3 >> [7] IRanges_1.19.1 >> [8] BiocGenerics_0.7.0 >> [9] ggbio_1.9.2 >> [10] ggplot2_0.9.3.1 >> [11] BiocInstaller_1.11.0 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.17.0 Biostrings_2.29.0 bitops_1.0-5 >> [4] BSgenome_1.29.0 cluster_1.14.4 colorspace_1.2-1 >> [7] DBI_0.2-5 dichromat_2.0-0 digest_0.6.3 >> [10] grid_3.1.0 gridExtra_0.9.1 gtable_0.1.2 >> [13] Hmisc_3.10-1 labeling_0.1 lattice_0.20-15 >> [16] MASS_7.3-26 munsell_0.4 plyr_1.8 >> [19] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> [22] reshape2_1.2.2 Rsamtools_1.13.1 RSQLite_0.11.2 >> [25] rtracklayer_1.21.0 scales_0.2.3 stats4_3.1.0 >> [28] stringr_0.6.2 tools_3.1.0 VariantAnnotation_1.7.4 >> [31] XML_3.96-1.1 zlibbioc_1.7.0 > > > > -- > Tengfei Yin > MCDB PhD student > 1620 Howe Hall, 2274, > Iowa State University > Ames, IA,50011-2274 -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
