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

[Julian Gehring]

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