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

[Tengfei Yin]

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 <yintengfei at gmail.com> 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 <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



-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274