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 _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
