[Bioc-devel] ggbio: autoplot(TranscriptDb) slow at certain regions

[Tengfei Yin]

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 <julian.gehring at embl.de> 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