[BioC] ggbio 1.12.0 autoplot() with txdb example is broken

Leonardo Collado Torres lcollado at jhu.edu
Wed Apr 30 04:05:48 CEST 2014


Hi Tengfei,

Interesting, I don't really know what's the issue with the bug you found.



Looking into ggbio 1.12.3 I noticed a couple of things with autoplot(txdb).

Basically, I found three cases.

Case 1: function works well, just a message that looks like a warning
(it's a message) is printed out. Nothing biggie.
Case 2: Labels when using tx_name(gene_id) don't work (although they
work in case 1) but they do work individually.
Case 3: Function fails because there is nothing in that region.

The code is shown below where you only have to specify the region of
interest according to the case.



Previously, I would use something like this (shown below) to catch case 3.

p.transcripts <- tryCatch(autoplot(txdb, which = wh,
            names.expr = "tx_name(gene_id)"), warning = function(w) {
            FALSE
        })

Now that it results in an error, I can detect these cases using:

p.transcripts <- tryCatch(autoplot(txdb, which = wh,
            names.expr = "tx_name(gene_id)"), error = function(e) {
            FALSE
        })


However, I thought that this would be a good time to report this.


Regarding case 2, in my use case I'm thinking of switching to
"tx_name" instead of using "tx_name(gene_id)". But well, it's also
worth reporting.



## Case 1 & 2 show the following 'message' that looks like a warning though

"gap" is not matching to following arbitrary model terms"cds CDS Cds
exon EXON Exon utr UTR Utr"

## Case 3 error

Error in data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms,  :
  arguments imply differing number of rows: 0, 1
> traceback()
13: stop(gettextf("arguments imply differing number of rows: %s",
        paste(unique(nrows), collapse = ", ")), domain = NA)
12: data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms,
        type = "exon")
11: .local(obj, ...)
10: crunch(data, which, truncate.gaps = truncate.gaps, truncate.fun =
truncate.fun,
        ratio = ratio, columns = columns)
9: crunch(data, which, truncate.gaps = truncate.gaps, truncate.fun =
truncate.fun,
       ratio = ratio, columns = columns)
8: .local(data, ...)
7: (function (data, ...)
   standardGeneric("geom_alignment"))(data = <S4 object of class
"TranscriptDb">,
       truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment",
       stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE,
       which = <S4 object of class "GRanges">, list())
6: (function (data, ...)
   standardGeneric("geom_alignment"))(data = <S4 object of class
"TranscriptDb">,
       truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment",
       stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE,
       which = <S4 object of class "GRanges">, list())
5: do.call(geom_alignment, args.res)
4: do.call(geom_alignment, args.res)
3: .local(object, ...)
2: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)")
1: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)")



Here's the code.



## Load required libs
library(ggbio)
library(GenomicRanges)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

### Set up region

## Case 1: Labels don't work for tx_name(gene_id) case
# wh <- GRanges("chr21", ranges=IRanges(start=47411800, end=47412600))
## Case 2: Labels work, although what looks like a warning is still shown
# wh <- GRanges("chr17", ranges=IRanges(start=47115000, end=47130000))
## Case 3: Error
wh <- GRanges("chr21", ranges=IRanges(start=36759003, end=36800825))

p1 <- autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)")
p2 <- autoplot(txdb, which = wh, names.expr = "tx_name")
p3 <- autoplot(txdb, which = wh, names.expr = "gene_id")

chr <- as.character(seqnames(wh))


## load the ideogram info
hg19IdeogramCyto <- NULL
load(system.file("data", "hg19IdeogramCyto.rda", package =
"biovizBase", mustWork = TRUE))
p.ideogram <- plotIdeogram(hg19IdeogramCyto, chr)

## Combine info into a tracks plot
p.final <-  tracks(p.ideogram, `tx_name\n(gene_id)` = p1, `tx_name` =
p2, `gene_id` = p3, heights = c(2, 3, 3, 3), xlim = wh, title =
"test") + ylab("") + theme_tracks_sunset()
p.final








> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
 [1] XVector_0.4.0
TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
 [3] GenomicFeatures_1.16.0                   AnnotationDbi_1.26.0
 [5] Biobase_2.24.0                           GenomicRanges_1.16.2
 [7] GenomeInfoDb_1.0.2                       IRanges_1.22.4
 [9] ggbio_1.12.3                             ggplot2_0.9.3.1
[11] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] BatchJobs_1.2            BBmisc_1.6               BiocParallel_0.6.0
 [4] biomaRt_2.20.0           Biostrings_2.32.0        biovizBase_1.12.1
 [7] bitops_1.0-6             brew_1.0-6               BSgenome_1.32.0
[10] cluster_1.15.2           codetools_0.2-8          colorspace_1.2-4
[13] DBI_0.2-7                dichromat_2.0-0          digest_0.6.4
[16] fail_1.2                 foreach_1.4.2            Formula_1.1-1
[19] GenomicAlignments_1.0.0  grid_3.1.0               gridExtra_0.9.1
[22] gtable_0.1.2             Hmisc_3.14-4             iterators_1.0.7
[25] lattice_0.20-29          latticeExtra_0.6-26      MASS_7.3-32
[28] munsell_0.4.2            plyr_1.8.1               proto_0.3-10
[31] RColorBrewer_1.0-5       Rcpp_0.11.1              RCurl_1.95-4.1
[34] reshape2_1.4             Rsamtools_1.16.0         RSQLite_0.11.4
[37] rtracklayer_1.24.0       scales_0.2.4             sendmailR_1.1-2
[40] splines_3.1.0            stats4_3.1.0             stringr_0.6.2
[43] survival_2.37-7          tools_3.1.0              VariantAnnotation_1.10.0
[46] XML_3.98-1.1             zlibbioc_1.10.0




Cheers,
Leo

On Tue, Apr 29, 2014 at 9:03 PM, Tengfei Yin <tengfei.yin at sbgenomics.com> wrote:
> it's good it's building, but it's very weird that it works, because I simply
> removed eval = TRUE for that chunk which is default. I came across some
> really weird *bug* in knitr which I try to reproduce with a minimal example,
> if you look closely, I put three blank code chunk at the front to avoid the
> figures orders being messed up somehow and I don't know why. I guess until I
> have a minimal example, I cannot really report it to yihui to fix it.
>
>
> On Tue, Apr 29, 2014 at 7:03 PM, Leonardo Collado Torres
> <lcollado at jhsph.edu> wrote:
>>
>> I just noticed that ggbio is building now
>>
>> http://www.bioconductor.org/checkResults/release/bioc-LATEST/ggbio/zin2-buildsrc.html
>> and I'm happy to report that the problem I mentioned is resolved with
>> ggbio 1.12.3. Thank you Tengfei and Dan!
>>
>>
>> For reference, here is the working session information.
>>
>> > sessionInfo()
>> R version 3.1.0 (2014-04-10)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets
>> methods   base
>>
>> other attached packages:
>>  [1] XVector_0.4.0
>> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
>>  [3] GenomicFeatures_1.16.0                   AnnotationDbi_1.26.0
>>  [5] Biobase_2.24.0                           GenomicRanges_1.16.2
>>  [7] GenomeInfoDb_1.0.2                       IRanges_1.22.4
>>  [9] ggbio_1.12.3                             ggplot2_0.9.3.1
>> [11] BiocGenerics_0.10.0
>>
>> loaded via a namespace (and not attached):
>>  [1] BatchJobs_1.2            BBmisc_1.6               BiocParallel_0.6.0
>>  [4] biomaRt_2.20.0           Biostrings_2.32.0        biovizBase_1.12.1
>>  [7] bitops_1.0-6             brew_1.0-6               BSgenome_1.32.0
>> [10] cluster_1.15.2           codetools_0.2-8          colorspace_1.2-4
>> [13] DBI_0.2-7                dichromat_2.0-0          digest_0.6.4
>> [16] fail_1.2                 foreach_1.4.2            Formula_1.1-1
>> [19] GenomicAlignments_1.0.0  grid_3.1.0               gridExtra_0.9.1
>> [22] gtable_0.1.2             Hmisc_3.14-4             iterators_1.0.7
>> [25] labeling_0.2             lattice_0.20-29          latticeExtra_0.6-26
>> [28] MASS_7.3-32              munsell_0.4.2            plyr_1.8.1
>> [31] proto_0.3-10             RColorBrewer_1.0-5       Rcpp_0.11.1
>> [34] RCurl_1.95-4.1           reshape2_1.4             Rsamtools_1.16.0
>> [37] RSQLite_0.11.4           rtracklayer_1.24.0       scales_0.2.4
>> [40] sendmailR_1.1-2          splines_3.1.0            stats4_3.1.0
>> [43] stringr_0.6.2            survival_2.37-7          tools_3.1.0
>> [46] VariantAnnotation_1.10.0 XML_3.98-1.1             zlibbioc_1.10.0
>>
>> On Sat, Apr 26, 2014 at 10:45 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>> wrote:
>> >
>> >
>> > ----- Original Message -----
>> >> From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
>> >> To: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
>> >> Cc: lcollado at jhu.edu, "Bioconductor mailing list"
>> >> <bioconductor at r-project.org>
>> >> Sent: Saturday, April 26, 2014 7:33:41 PM
>> >> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
>> >>
>> >>
>> >>
>> >> ----- Original Message -----
>> >> > From: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
>> >> > To: lcollado at jhu.edu
>> >> > Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Bioconductor mailing
>> >> > list" <bioconductor at r-project.org>
>> >> > Sent: Saturday, April 26, 2014 1:58:01 PM
>> >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is
>> >> > broken
>> >> >
>> >> >
>> >> > right, it's failing to build and I am trying to figure out why now,
>> >> > because it passes check/build and works on my laptop, but it
>> >> > doesn't
>> >> > pass bioc build for both release and devel, let me dig into it
>> >> > tonight.
>> >> >
>> >>
>> >> Seems like this could be fixed if you just add
>> >>
>> >> library(ggbio)
>> >>
>> >> to your vignette before the ggbio() function is called on line 557 of
>> >> vignettes/realvignettes/ggbio.Rnw.
>> >>
>> >
>> > Sorry, I spoke too soon; that just changes the error message you
>> > receive.
>> > Dan
>> >
>> >
>> >> Dan
>> >>
>> >>
>> >> >
>> >> > thanks for your patience
>> >> >
>> >> >
>> >> > Tengfei
>> >> >
>> >> >
>> >> >
>> >> > On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres <
>> >> > lcollado at jhsph.edu > wrote:
>> >> >
>> >> >
>> >> >
>> >> > Oh ok. Thanks for the info
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum <
>> >> > dtenenba at fhcrc.org
>> >> > > wrote:
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > Leonardo Collado Torres < lcollado at jhsph.edu > wrote:
>> >> >
>> >> > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC
>> >> > >release?
>> >> > >
>> >> > > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html
>> >> > >still
>> >> > >points to 1.12.0
>> >> > >
>> >> >
>> >> > It's failing to build:
>> >> >
>> >> >
>> >> > http://www.bioconductor.org/checkResults/release/bioc-LATEST/ggbio/zin2-buildsrc.html
>> >> >
>> >> >
>> >> >
>> >> > Dan
>> >> >
>> >> > >
>> >> > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum <
>> >> > >dtenenba at fhcrc.org
>> >> > >>
>> >> > >wrote:
>> >> > >
>> >> > >>
>> >> > >>
>> >> > >> ----- Original Message -----
>> >> > >> > From: "Leonardo Collado Torres" < lcollado at jhsph.edu >
>> >> > >> > To: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>> >> > >> > Cc: "Dan Tenenbaum" < dtenenba at fhcrc.org >, "Bioconductor
>> >> > >> > mailing
>> >> > >list" <
>> >> > >> bioconductor at r-project.org >
>> >> > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM
>> >> > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example
>> >> > >> > is
>> >> > >broken
>> >> > >> >
>> >> > >> > Dang it, forgot again to send with my @ jhsph.edu account. See
>> >> > >> > below
>> >> > >> > again >.<
>> >> > >> >
>> >> > >> > On the email topic, is it possible to be subscribed with 2
>> >> > >> > emails
>> >> > >> > accounts to the BioC mailing list but only get emails with
>> >> > >> > one?
>> >> > >> > I
>> >> > >> > believe that I have to choose to either get the daily digest
>> >> > >> > or
>> >> > >> > get
>> >> > >a
>> >> > >> > single for every message sent. If not, I'll probably just drop
>> >> > >> > my
>> >> > >> > @ jhsph.edu subscription and re-subscribe with the new @
>> >> > >> > jhu.edu
>> >> > >> > mail
>> >> > >I
>> >> > >> > got (our university is pushing these mails).
>> >> > >> >
>> >> > >>
>> >> > >> I don't know; you could try it. Another option would be to
>> >> > >> configure
>> >> > >your
>> >> > >> mail client with a filter to drop the undesired bioc emails.
>> >> > >>
>> >> > >> Dan
>> >> > >>
>> >> > >>
>> >> > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres
>> >> > >> > < lcollado at jhu.edu > wrote:
>> >> > >> > > Hi Dan,
>> >> > >> > >
>> >> > >> > > I got RSwitch to work with a second installation of R 3.1.
>> >> > >> > > Basically,
>> >> > >> > > I downloaded the leopard tarball, expanded it, renamed the
>> >> > >> > > folder
>> >> > >> > > 3.1
>> >> > >> > > to 3.1patched (which is the version I downloaded, but well,
>> >> > >> > > anything
>> >> > >> > > except for 3.1 would work), compressed it again, and then
>> >> > >expanded
>> >> > >> > > it
>> >> > >> > > at the root location.
>> >> > >> > >
>> >> > >> > > So it would be something like this:
>> >> > >> > >
>> >> > >> > > wget
>> >> > >> > >
>> >> > >>
>> >> > >
>> >> > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch-snowleopard-sa-x86_64.tar.gz
>> >> > >> > > tar -xvf R-*gz
>> >> > >> > > mv Library/Frameworks/R.framework/Versions/3.1
>> >> > >> > > Library/Frameworks/R.framework/Versions/3.1patched
>> >> > >> > > tar -cvzf Rlib.tgz Library
>> >> > >> > > sudo tar fvxz Rlib.tgz -C /
>> >> > >> > >
>> >> > >> > > Then used RSwitch, and was able to install BioC-devel.
>> >> > >> > >
>> >> > >> > > I might try out your `renv` at a different time. It's great
>> >> > >> > > to
>> >> > >know
>> >> > >> > > that it exists =)
>> >> > >> > >
>> >> > >> > > Cheers,
>> >> > >> > > Leo
>> >> > >> > >
>> >> > >> > >
>> >> > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin
>> >> > >> > > < tengfei.yin at sbgenomics.com > wrote:
>> >> > >> > >> Hi Dan,
>> >> > >> > >>
>> >> > >> > >> It works like a charm, thanks!
>> >> > >> > >>
>> >> > >> > >> I use your method, then I changed /Library/Framework/
>> >> > >> > >> folder
>> >> > >> > >> and
>> >> > >> > >> R.Framework
>> >> > >> > >> folder ownership to myself so I don't have to sudo it, then
>> >> > >> > >> I
>> >> > >just
>> >> > >> > >> add alias
>> >> > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R
>> >> > >> > >> first.
>> >> > >> > >> This solves
>> >> > >> > >> my problem.
>> >> > >> > >>
>> >> > >> > >> Try to customize variable for R hooks in emacs as
>> >> > >> > >> alternative
>> >> > >> > >> solution, but
>> >> > >> > >> may need more time.
>> >> > >> > >>
>> >> > >> > >> Thanks again!
>> >> > >> > >>
>> >> > >> > >> Tengfei
>> >> > >> > >>
>> >> > >> > >>
>> >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum
>> >> > >> > >> < dtenenba at fhcrc.org > wrote:
>> >> > >> > >>>
>> >> > >> > >>> Hi Tengfei,
>> >> > >> > >>>
>> >> > >> > >>> ----- Original Message -----
>> >> > >> > >>> > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>> >> > >> > >>> > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
>> >> > >> > >>> > Cc: "Bioconductor mailing list" <
>> >> > >> > >>> > bioconductor at r-project.org >,
>> >> > >> > >>> > lcollado at jhu.edu
>> >> > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM
>> >> > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb
>> >> > >> > >>> > example
>> >> > >> > >>> > is broken
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all
>> >> > >> > >>> > on
>> >> > >the
>> >> > >> > >>> > R 3.1?
>> >> > >> > >>>
>> >> > >> > >>> Yes, install two copies of R 3.1 and switch between them.
>> >> > >> > >>>
>> >> > >> > >>> > And do some sort of switch for bioc? The website you
>> >> > >> > >>> > send
>> >> > >> > >>> > to
>> >> > >me
>> >> > >> > >>> > also
>> >> > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on
>> >> > >R-devel
>> >> > >> > >>> > and
>> >> > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R
>> >> > >> > >>> > only
>> >> > >to
>> >> > >> > >>> > switch bioc, so that I could debug and maintain released
>> >> > >> > >>> > and
>> >> > >> > >>> > devel
>> >> > >> > >>> > version.
>> >> > >> > >>>
>> >> > >> > >>> PLEASE don't use R-devel at all.
>> >> > >> > >>>
>> >> > >> > >>> Just use R-3.1.0.
>> >> > >> > >>>
>> >> > >> > >>> You can use the Rswitch app but as you point out it won't
>> >> > >> > >>> work
>> >> > >> > >>> within
>> >> > >> > >>> emacs.
>> >> > >> > >>>
>> >> > >> > >>> This is what I do:
>> >> > >> > >>>
>> >> > >> > >>> Every time I download a new version of R, I run its
>> >> > >> > >>> installer.
>> >> > >> > >>> The
>> >> > >> > >>> installer always puts it in
>> >> > >> > >>>
>> >> > >> > >>> /Library/Frameworks/R.framework
>> >> > >> > >>>
>> >> > >> > >>> So after I install each version of R, I rename the
>> >> > >> > >>> R.framework
>> >> > >> > >>> directory
>> >> > >> > >>> to something like
>> >> > >> > >>> R.framework.bioc214_snowleopard
>> >> > >> > >>>
>> >> > >> > >>> And then I make a symlink from
>> >> > >> > >>> R.framework.bioc214_snowleopard
>> >> > >to
>> >> > >> > >>> R.framework.
>> >> > >> > >>>
>> >> > >> > >>> I have a little script at https://github.com/dtenenba/renv
>> >> > >which
>> >> > >> > >>> lets me
>> >> > >> > >>> see what the various installed Rs are:
>> >> > >> > >>>
>> >> > >> > >>> $ renv
>> >> > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0
>> >> > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
>> >> > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
>> >> > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
>> >> > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
>> >> > >> > >>>
>> >> > >> > >>> This tells me that the currently active R is nicknamed
>> >> > >> > >>> "releaseMav" (this
>> >> > >> > >>> means there is a link from
>> >> > >> > >>> /Library/Frameworks/R.framework.releaseMav to
>> >> > >> > >>> /Library/Frameworks/R.framework. It shows the versions,
>> >> > >> > >>> svn
>> >> > >> > >>> revisions,
>> >> > >> > >>> dates, and architectures of each version. (darwin10.8.0 is
>> >> > >> > >>> Snow
>> >> > >> > >>> Leopard;
>> >> > >> > >>> darwin13.1.0 is Mavericks).
>> >> > >> > >>>
>> >> > >> > >>> Note that in my nomenclature devel means BioC devel, not
>> >> > >R-devel.
>> >> > >> > >>>
>> >> > >> > >>> So if I wanted to switch to the "develSL" version I would
>> >> > >> > >>> do:
>> >> > >> > >>>
>> >> > >> > >>> sudo renv develSL
>> >> > >> > >>>
>> >> > >> > >>> HTH
>> >> > >> > >>> Dan
>> >> > >> > >>>
>> >> > >> > >>>
>> >> > >> > >>>
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum <
>> >> > >> > >>> > dtenenba at fhcrc.org >
>> >> > >> > >>> > wrote:
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> > Hi Tengfei,
>> >> > >> > >>> >
>> >> > >> > >>> > ----- Original Message -----
>> >> > >> > >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>> >> > >> > >>> >
>> >> > >> > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
>> >> > >> > >>> > > Cc: "Bioconductor mailing list" <
>> >> > > bioconductor at r-project.org
>> >> > >> > >>> > > >,
>> >> > >> > >>> > > lcollado at jhu.edu
>> >> > >> > >>> >
>> >> > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM
>> >> > >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb
>> >> > >example
>> >> > >> > >>> > > is
>> >> > >> > >>> > > broken
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> >
>> >> > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I
>> >> > >> > >>> > > am
>> >> > >still
>> >> > >> > >>> > > a
>> >> > >> > >>> > > newbie to OSX ... I got R-devel running and I will try
>> >> > >> > >>> > > Rswitcher, I
>> >> > >> > >>> > > also want to do that switch easily in emacs too.
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> >
>> >> > >> > >>> > You don't want to use R-devel. Both BioC release (2.14)
>> >> > >> > >>> > and
>> >> > >> > >>> > BioC
>> >> > >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released
>> >> > >> > >>> > version of
>> >> > >> > >>> > R.
>> >> > >> > >>> >
>> >> > >> > >>> > I think the Rswitch app just sets a symbolic link, so
>> >> > >> > >>> > you
>> >> > >> > >>> > should be
>> >> > >> > >>> > able to do that within emacs. Run it and see what it
>> >> > >> > >>> > does
>> >> > >> > >>> > to
>> >> > >> > >>> > /Library/Frameworks/R.framework.
>> >> > >> > >>> >
>> >> > >> > >>> > Dan
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> > >
>> >> > >> > >>> > > cheers
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > > Tengfei
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum <
>> >> > >> > >>> > > dtenenba at fhcrc.org
>> >> > >> > >>> > > >
>> >> > >> > >>> > > wrote:
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > > ----- Original Message -----
>> >> > >> > >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>> >> > >> > >>> > >
>> >> > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
>> >> > >> > >>> > > > Cc: "Bioconductor mailing list" <
>> >> > >> > >>> > > > bioconductor at r-project.org >,
>> >> > >> > >>> > > > lcollado at jhu.edu
>> >> > >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM
>> >> > >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with
>> >> > >> > >>> > > > txdb
>> >> > >> > >>> > > > example is
>> >> > >> > >>> > > > broken
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > >
>> >> > >> > >>> > > > Hi Dan,
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it
>> >> > >should
>> >> > >> > >>> > > > work?
>> >> > >> > >>> > >
>> >> > >> > >>> > > Yes.
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > > ? Is
>> >> > >> > >>> > > > there a way to build from source using biocLite,
>> >> > >> > >>> > > > like
>> >> > >type
>> >> > >> > >>> > > > =
>> >> > >> > >>> > > > "source", this is what I got
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > > library(BiocInstaller)
>> >> > >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1),
>> >> > >?biocLite
>> >> > >> > >>> > > > for
>> >> > >> > >>> > > > help
>> >> > >> > >>> > > > > biocLite("GenomicRanges")
>> >> > >> > >>> > > > BioC_mirror: http://bioconductor.org
>> >> > >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller
>> >> > >> > >>> > > > 1.14.1), R
>> >> > >> > >>> > > > version
>> >> > >> > >>> > > > 3.1.0.
>> >> > >> > >>> > > > Installing package(s) 'GenomicRanges'
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > package ‘GenomicRanges’ is available as a source
>> >> > >> > >>> > > > package
>> >> > >> > >>> > > > but not
>> >> > >> > >>> > > > as
>> >> > >> > >>> > > > a
>> >> > >> > >>> > > > binary
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > Warning message:
>> >> > >> > >>> > > > package ‘GenomicRanges’ is not available (for R
>> >> > >> > >>> > > > version
>> >> > >> > >>> > > > 3.1.0)
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > Just wondering is there a solution without
>> >> > >> > >>> > > > re-install
>> >> > >> > >>> > > > R
>> >> > >for
>> >> > >> > >>> > > > snow
>> >> > >> > >>> > > > leopard. And what's the plan for maverick?
>> >> > >> > >>> > > >
>> >> > >> > >>> > >
>> >> > >> > >>> > > You can do
>> >> > >> > >>> > > biocLite("GenomicRanges", type="source")
>> >> > >> > >>> > >
>> >> > >> > >>> > > but you need to have the appropriate compilers, etc.
>> >> > >> > >>> > >
>> >> > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build.
>> >> > >> > >>> > > You
>> >> > >can
>> >> > >> > >>> > > have
>> >> > >> > >>> > > multiple installations of R on your Mac and switch
>> >> > >> > >>> > > between
>> >> > >> > >>> > > them
>> >> > >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or
>> >> > >another
>> >> > >> > >>> > > easy
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> > > mechanism.
>> >> > >> > >>> > >
>> >> > >> > >>> > > We are building packages for Mavericks now, we just
>> >> > >> > >>> > > have
>> >> > >> > >>> > > to
>> >> > >> > >>> > > resolve
>> >> > >> > >>> > > a
>> >> > >> > >>> > > few build issues and test the resulting packages, we
>> >> > >> > >>> > > still
>> >> > >> > >>> > > hope to
>> >> > >> > >>> > > have them available by the end of the month. But since
>> >> > >> > >>> > > you
>> >> > >> > >>> > > can
>> >> > >> > >>> > > install the Snow Leopard build without needing to
>> >> > >> > >>> > > remove
>> >> > >your
>> >> > >> > >>> > > Mavericks build, you should do that.
>> >> > >> > >>> > >
>> >> > >> > >>> > > Dan
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > Thanks
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > Tengfei
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum <
>> >> > >> > >>> > > > dtenenba at fhcrc.org
>> >> > >> > >>> > > > > wrote:
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > Hi Tengfei,
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > ----- Original Message -----
>> >> > >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>> >> > >> > >>> > > > > To: lcollado at jhu.edu
>> >> > >> > >>> > > > > Cc: bioconductor at r-project.org
>> >> > >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM
>> >> > >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with
>> >> > >> > >>> > > > > txdb
>> >> > >> > >>> > > > > example
>> >> > >> > >>> > > > > is
>> >> > >> > >>> > > > > broken
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > > btw, based on the error, let me try to debug it.
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin
>> >> > >> > >>> > > > > < tengfei.yin at sbgenomics.com >wrote:
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > > > Hi Leonardo,
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > > Frankly speaking, the vignette is still in
>> >> > >> > >>> > > > > > progress,
>> >> > >> > >>> > > > > > and
>> >> > >> > >>> > > > > > there
>> >> > >> > >>> > > > > > are
>> >> > >> > >>> > > > > > some
>> >> > >> > >>> > > > > > known bugs in ggbio I need to fix (still trying
>> >> > >> > >>> > > > > > to
>> >> > >find
>> >> > >> > >>> > > > > > a
>> >> > >> > >>> > > > > > time
>> >> > >> > >>> > > > > > to
>> >> > >> > >>> > > > > > do that
>> >> > >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and
>> >> > >> > >>> > > > > > Bioc
>> >> > >> > >>> > > > > > 2.14 on
>> >> > >> > >>> > > > > > my
>> >> > >> > >>> > > > > > new MBP
>> >> > >> > >>> > > > > > with OSX 10.9, but fails, probably binary build
>> >> > >> > >>> > > > > > is
>> >> > >not
>> >> > >> > >>> > > > > > ready
>> >> > >> > >>> > > > > > for
>> >> > >> > >>> > > > > > maverick
>> >> > >> > >>> > > > > > yet, maybe available by the end of April?
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > > Thanks for reporting the bug, I will keep you
>> >> > >> > >>> > > > > > posted
>> >> > >on
>> >> > >> > >>> > > > > > this
>> >> > >> > >>> > > > > > when
>> >> > >> > >>> > > > > > I
>> >> > >> > >>> > > > > > successfully get it on my laptop and start
>> >> > >> > >>> > > > > > fixing
>> >> > >> > >>> > > > > > the
>> >> > >> > >>> > > > > > problems.
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > You can install the Snow Leopard build of R and
>> >> > >> > >>> > > > should
>> >> > >have
>> >> > >> > >>> > > > no
>> >> > >> > >>> > > > problems, binary packages are available for that
>> >> > >> > >>> > > > version.
>> >> > >> > >>> > > > It will
>> >> > >> > >>> > > > run fine on Mavericks.
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > Dan
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > > > cheers
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > > Tengfei
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo
>> >> > >> > >>> > > > > > Collado
>> >> > >> > >>> > > > > > Torres <
>> >> > >> > >>> > > > > > lcollado at jhsph.edu > wrote:
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > >> Hello Tengfei + bioc list,
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> From
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >>
>> >> > >>
>> >> > >
>> >> > > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf
>> >> > >> > >>> > > > > >> page 4 (complied on april 11 2014), the
>> >> > >> > >>> > > > > >> following
>> >> > >> > >>> > > > > >> example
>> >> > >> > >>> > > > > >> loads
>> >> > >> > >>> > > > > >> to
>> >> > >> > >>> > > > > >> an
>> >> > >> > >>> > > > > >> error as shown below. I wasn't seeing this
>> >> > >> > >>> > > > > >> error
>> >> > >> > >>> > > > > >> before
>> >> > >> > >>> > > > > >> (aka,
>> >> > >> > >>> > > > > >> last
>> >> > >> > >>> > > > > >> week). The only guess that comes to mind is the
>> >> > >recent
>> >> > >> > >>> > > > > >> update
>> >> > >> > >>> > > > > >> to
>> >> > >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't
>> >> > >> > >>> > > > > >> seem
>> >> > >> > >>> > > > > >> to
>> >> > >> > >>> > > > > >> be
>> >> > >> > >>> > > > > >> related
>> >> > >> > >>> > > > > >> from
>> >> > >> > >>> > > > > >> the traceback() output, well... maybe it's
>> >> > >> > >>> > > > > >> related
>> >> > >to
>> >> > >> > >>> > > > > >> the
>> >> > >> > >>> > > > > >> ignore.strand = TRUE part as described in the
>> >> > >> > >>> > > > > >> error.
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> I'll create a GitHub issue just for
>> >> > >> > >>> > > > > >> completeness.
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> Thank you,
>> >> > >> > >>> > > > > >> Leonardo
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> > library(ggbio)
>> >> > >> > >>> > > > > >> ## Removed the output, nothing out of ordinary
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>> >> > >> > >>> > > > > >> ## Removed the output
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>> >> > >> > >>> > > > > >> > data(genesymbol, package = "biovizBase")
>> >> > >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which =
>> >> > >> > >>> > > > > >> > genesymbol["BRCA1"])
>> >> > >> > >>> > > > > >> Aggregating TranscriptDb...
>> >> > >> > >>> > > > > >> Parsing transcripts...
>> >> > >> > >>> > > > > >> Parsing exons...
>> >> > >> > >>> > > > > >> Parsing cds...
>> >> > >> > >>> > > > > >> Parsing utrs...
>> >> > >> > >>> > > > > >> ------exons...
>> >> > >> > >>> > > > > >> ------cdss...
>> >> > >> > >>> > > > > >> ------introns...
>> >> > >> > >>> > > > > >> ------utr...
>> >> > >> > >>> > > > > >> aggregating...
>> >> > >> > >>> > > > > >> Done
>> >> > >> > >>> > > > > >> Constructing graphics...
>> >> > >> > >>> > > > > >> Error in sapply(listData, function(Xi)
>> >> > >> > >>> > > > > >> extends(class(Xi),
>> >> > >> > >>> > > > > >> elementTypeX)) :
>> >> > >> > >>> > > > > >> error in evaluating the argument 'X' in
>> >> > >> > >>> > > > > >> selecting
>> >> > >> > >>> > > > > >> a
>> >> > >> > >>> > > > > >> method
>> >> > >> > >>> > > > > >> for
>> >> > >> > >>> > > > > >> function 'sapply': Error in
>> >> > >> > >>> > > > > >> unlist(range(ranges(x.n,
>> >> > >> > >>> > > > > >> ignore.strand
>> >> > >> > >>> > > > > >> =
>> >> > >> > >>> > > > > >> TRUE))) :
>> >> > >> > >>> > > > > >> error in evaluating the argument 'x' in
>> >> > >> > >>> > > > > >> selecting
>> >> > >> > >>> > > > > >> a
>> >> > >> > >>> > > > > >> method
>> >> > >> > >>> > > > > >> for
>> >> > >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) :
>> >> > >> > >>> > > > > >> unused
>> >> > >> > >>> > > > > >> argument
>> >> > >> > >>> > > > > >> (ignore.strand = TRUE)
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> > traceback()
>> >> > >> > >>> > > > > >> 15: sapply(listData, function(Xi)
>> >> > >> > >>> > > > > >> extends(class(Xi),
>> >> > >> > >>> > > > > >> elementTypeX))
>> >> > >> > >>> > > > > >> 14: .updateCompressedList(X,
>> >> > >lapply_CompressedList(X,
>> >> > >> > >>> > > > > >> FUN,
>> >> > >> > >>> > > > > >> ...))
>> >> > >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) {
>> >> > >> > >>> > > > > >> if (!is.null( group.name )) {
>> >> > >> > >>> > > > > >> if (!group.selfish) {
>> >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ])
>> >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand =
>> >> > >> > >>> > > > > >> TRUE)))
>> >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width =
>> >> > >> > >>> > > > > >> width(irs) +
>> >> > >> > >>> > > > > >> extend.size)
>> >> > >> > >>> > > > > >> irs.new <- sort(irs.new)
>> >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new)
>> >> > >> > >>> > > > > >> values(x)$stepping <-
>> >> > >> > >>> > > > > >> .lvs[as.character(values(x)[,
>> >> > >> > >>> > > > > >> group.name ])]
>> >> > >> > >>> > > > > >> x
>> >> > >> > >>> > > > > >> }
>> >> > >> > >>> > > > > >> else {
>> >> > >> > >>> > > > > >> values(x)$stepping <-
>> >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[,
>> >> > >> > >>> > > > > >> group.name ]))
>> >> > >> > >>> > > > > >> x
>> >> > >> > >>> > > > > >> }
>> >> > >> > >>> > > > > >> }
>> >> > >> > >>> > > > > >> else {
>> >> > >> > >>> > > > > >> irs <- ranges(x)
>> >> > >> > >>> > > > > >> values(x)$stepping <-
>> >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs,
>> >> > >> > >>> > > > > >> fix = "center", width = width(irs) +
>> >> > >> > >>> > > > > >> extend.size)))
>> >> > >> > >>> > > > > >> x
>> >> > >> > >>> > > > > >> }
>> >> > >> > >>> > > > > >> })
>> >> > >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) {
>> >> > >> > >>> > > > > >> if (!is.null( group.name )) {
>> >> > >> > >>> > > > > >> if (!group.selfish) {
>> >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ])
>> >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand =
>> >> > >> > >>> > > > > >> TRUE)))
>> >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width =
>> >> > >> > >>> > > > > >> width(irs) +
>> >> > >> > >>> > > > > >> extend.size)
>> >> > >> > >>> > > > > >> irs.new <- sort(irs.new)
>> >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new)
>> >> > >> > >>> > > > > >> values(x)$stepping <-
>> >> > >> > >>> > > > > >> .lvs[as.character(values(x)[,
>> >> > >> > >>> > > > > >> group.name ])]
>> >> > >> > >>> > > > > >> x
>> >> > >> > >>> > > > > >> }
>> >> > >> > >>> > > > > >> else {
>> >> > >> > >>> > > > > >> values(x)$stepping <-
>> >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[,
>> >> > >> > >>> > > > > >> group.name ]))
>> >> > >> > >>> > > > > >> x
>> >> > >> > >>> > > > > >> }
>> >> > >> > >>> > > > > >> }
>> >> > >> > >>> > > > > >> else {
>> >> > >> > >>> > > > > >> irs <- ranges(x)
>> >> > >> > >>> > > > > >> values(x)$stepping <-
>> >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs,
>> >> > >> > >>> > > > > >> fix = "center", width = width(irs) +
>> >> > >> > >>> > > > > >> extend.size)))
>> >> > >> > >>> > > > > >> x
>> >> > >> > >>> > > > > >> }
>> >> > >> > >>> > > > > >> })
>> >> > >> > >>> > > > > >> 11: .local(obj, ...)
>> >> > >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id",
>> >> > >> > >>> > > > > >> group.selfish =
>> >> > >> > >>> > > > > >> FALSE,
>> >> > >> > >>> > > > > >> fix = "start", extend.size = es)
>> >> > >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id",
>> >> > >group.selfish
>> >> > >> > >>> > > > > >> =
>> >> > >> > >>> > > > > >> FALSE,
>> >> > >> > >>> > > > > >> fix = "start", extend.size = es)
>> >> > >> > >>> > > > > >> 8: .local(data, ...)
>> >> > >> > >>> > > > > >> 7: (function (data, ...)
>> >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <S4
>> >> > >> > >>> > > > > >> object
>> >> > >> > >>> > > > > >> of
>> >> > >> > >>> > > > > >> class
>> >> > >> > >>> > > > > >> "TranscriptDb">,
>> >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom =
>> >> > >> > >>> > > > > >> "alignment",
>> >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name",
>> >> > >> > >>> > > > > >> label
>> >> > >> > >>> > > > > >> =
>> >> > >> > >>> > > > > >> TRUE,
>> >> > >> > >>> > > > > >> which = <S4 object of class "GRanges">, list())
>> >> > >> > >>> > > > > >> 6: (function (data, ...)
>> >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <S4
>> >> > >> > >>> > > > > >> object
>> >> > >> > >>> > > > > >> of
>> >> > >> > >>> > > > > >> class
>> >> > >> > >>> > > > > >> "TranscriptDb">,
>> >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom =
>> >> > >> > >>> > > > > >> "alignment",
>> >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name",
>> >> > >> > >>> > > > > >> label
>> >> > >> > >>> > > > > >> =
>> >> > >> > >>> > > > > >> TRUE,
>> >> > >> > >>> > > > > >> which = <S4 object of class "GRanges">, list())
>> >> > >> > >>> > > > > >> 5: do.call(geom_alignment, args.res)
>> >> > >> > >>> > > > > >> 4: do.call(geom_alignment, args.res)
>> >> > >> > >>> > > > > >> 3: .local(object, ...)
>> >> > >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"])
>> >> > >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"])
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> > sessionInfo()
>> >> > >> > >>> > > > > >> R version 3.1.0 (2014-04-10)
>> >> > >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> locale:
>> >> > >> > >>> > > > > >> [1]
>> >> > >> > >>> > > > > >>
>> >> > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> attached base packages:
>> >> > >> > >>> > > > > >> [1] parallel stats graphics grDevices utils
>> >> > >> > >>> > > > > >> datasets
>> >> > >> > >>> > > > > >> methods base
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> other attached packages:
>> >> > >> > >>> > > > > >> [1] XVector_0.4.0
>> >> > >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
>> >> > >> > >>> > > > > >> GenomicFeatures_1.16.0
>> >> > >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0
>> >> > >> > >>> > > > > >> GenomicRanges_1.16.2
>> >> > >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3
>> >> > >> > >>> > > > > >> ggbio_1.12.0
>> >> > >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >> loaded via a namespace (and not attached):
>> >> > >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5
>> >> > >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0
>> >> > >> > >>> > > > > >> Biostrings_2.32.0
>> >> > >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6
>> >> > >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2
>> >> > >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7
>> >> > >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4
>> >> > >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2
>> >> > >> > >>> > > > > >> Formula_1.1-1
>> >> > >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0
>> >> > >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2
>> >> > >> > >>> > > > > >> Hmisc_3.14-4
>> >> > >> > >>> > > > > >> iterators_1.0.7 labeling_0.2
>> >> > >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26
>> >> > >> > >>> > > > > >> MASS_7.3-31
>> >> > >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1
>> >> > >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5
>> >> > >> > >>> > > > > >> Rcpp_0.11.1
>> >> > >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2
>> >> > >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4
>> >> > >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2
>> >> > >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0
>> >> > >> > >>> > > > > >> stringr_0.6.2
>> >> > >> > >>> > > > > >> survival_2.37-7 tools_3.1.0
>> >> > >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1
>> >> > >> > >>> > > > > >> zlibbioc_1.10.0
>> >> > >> > >>> > > > > >> >
>> >> > >> > >>> > > > > >>
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > > > --
>> >> > >> > >>> > > > > > Tengfei Yin, PhD
>> >> > >> > >>> > > > > > Seven Bridges Genomics
>> >> > >> > >>> > > > > > sbgenomics.com
>> >> > >> > >>> > > > > > 625 Mt. Auburn St. Suite #208
>> >> > >> > >>> > > > > > Cambridge, MA 02138
>> >> > >> > >>> > > > > > (617) 866-0446
>> >> > >> > >>> > > > > >
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > > --
>> >> > >> > >>> > > > > Tengfei Yin, PhD
>> >> > >> > >>> > > > > Seven Bridges Genomics
>> >> > >> > >>> > > > > sbgenomics.com
>> >> > >> > >>> > > > > 625 Mt. Auburn St. Suite #208
>> >> > >> > >>> > > > > Cambridge, MA 02138
>> >> > >> > >>> > > > > (617) 866-0446
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > > [[alternative HTML version deleted]]
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > > > _______________________________________________
>> >> > >> > >>> > > > > Bioconductor mailing list
>> >> > >> > >>> > > > > Bioconductor at r-project.org
>> >> > >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> > >> > >>> > > > > Search the archives:
>> >> > >> > >>> > > > >
>> >> > >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >> > >> > >>> > > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > --
>> >> > >> > >>> > > >
>> >> > >> > >>> > > >
>> >> > >> > >>> > > > Tengfei Yin, PhD
>> >> > >> > >>> > > > Seven Bridges Genomics
>> >> > >> > >>> > > > sbgenomics.com
>> >> > >> > >>> > > > 625 Mt. Auburn St. Suite #208
>> >> > >> > >>> > > > Cambridge, MA 02138
>> >> > >> > >>> > > > (617) 866- 0446
>> >> > >> > >>> > > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > > --
>> >> > >> > >>> > >
>> >> > >> > >>> > >
>> >> > >> > >>> > > Tengfei Yin, PhD
>> >> > >> > >>> > > Seven Bridges Genomics
>> >> > >> > >>> > > sbgenomics.com
>> >> > >> > >>> > > 625 Mt. Auburn St. Suite #208
>> >> > >> > >>> > > Cambridge, MA 02138
>> >> > >> > >>> > > (617) 866- 0446
>> >> > >> > >>> > >
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> > --
>> >> > >> > >>> >
>> >> > >> > >>> >
>> >> > >> > >>> > Tengfei Yin, PhD
>> >> > >> > >>> > Seven Bridges Genomics
>> >> > >> > >>> > sbgenomics.com
>> >> > >> > >>> > 625 Mt. Auburn St. Suite #208
>> >> > >> > >>> > Cambridge, MA 02138
>> >> > >> > >>> > (617) 866- 0446
>> >> > >> > >>> >
>> >> > >> > >>
>> >> > >> > >>
>> >> > >> > >>
>> >> > >> > >>
>> >> > >> > >> --
>> >> > >> > >> Tengfei Yin, PhD
>> >> > >> > >> Seven Bridges Genomics
>> >> > >> > >> sbgenomics.com
>> >> > >> > >> 625 Mt. Auburn St. Suite #208
>> >> > >> > >> Cambridge, MA 02138
>> >> > >> > >> (617) 866-0446
>> >> > >> >
>> >> > >>
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> >
>> >> > Tengfei Yin, PhD
>> >> > Seven Bridges Genomics
>> >> > sbgenomics.com
>> >> > 625 Mt. Auburn St. Suite #208
>> >> > Cambridge, MA 02138
>> >> > (617) 866- 0446
>> >> >
>> >>
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor at r-project.org
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives:
>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>
> --
> Tengfei Yin, PhD
> Seven Bridges Genomics
> sbgenomics.com
> 625 Mt. Auburn St. Suite #208
> Cambridge, MA 02138
> (617) 866-0446



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