Hi Leo,
Thanks for reporting the bugs, yes, this is a perfect time to report,
if
you read a new updated vignette (still keep updating it ...) in 1.12.3
http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst
/doc/ggbio.pdf
You will notice section 'add gene model' changed, it support
OrganismDb
now, so the name.expr support more items now, if you are using
Homo.sapiens, you could label "gene symbols" too, I did lots of change
for
autoplot,Organism and autoplot,Txdb function, this will probably
introduce
some bugs you reported.
I will work on fixing those bugs you reported and keep you posted.
cheers
Tengfei
On Tue, Apr 29, 2014 at 10:05 PM, Leonardo Collado Torres
<lcollado@jhu.edu>wrote:
> 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@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@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@fhcrc.org>
> >> wrote:
> >> >
> >> >
> >> > ----- Original Message -----
> >> >> From: "Dan Tenenbaum" <dtenenba@fhcrc.org>
> >> >> To: "Tengfei Yin" <tengfei.yin@sbgenomics.com>
> >> >> Cc: lcollado@jhu.edu, "Bioconductor mailing list"
> >> >> <bioconductor@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@sbgenomics.com>
> >> >> > To: lcollado@jhu.edu
> >> >> > Cc: "Dan Tenenbaum" <dtenenba@fhcrc.org>, "Bioconductor
mailing
> >> >> > list" <bioconductor@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@jhsph.edu > wrote:
> >> >> >
> >> >> >
> >> >> >
> >> >> > Oh ok. Thanks for the info
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum <
> >> >> > dtenenba@fhcrc.org
> >> >> > > wrote:
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > Leonardo Collado Torres < lcollado@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@fhcrc.org
> >> >> > >>
> >> >> > >wrote:
> >> >> > >
> >> >> > >>
> >> >> > >>
> >> >> > >> ----- Original Message -----
> >> >> > >> > From: "Leonardo Collado Torres" < lcollado@jhsph.edu >
> >> >> > >> > To: "Tengfei Yin" < tengfei.yin@sbgenomics.com >
> >> >> > >> > Cc: "Dan Tenenbaum" < dtenenba@fhcrc.org >,
"Bioconductor
> >> >> > >> > mailing
> >> >> > >list" <
> >> >> > >> bioconductor@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@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@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@fhcrc.org > wrote:
> >> >> > >> > >>>
> >> >> > >> > >>> Hi Tengfei,
> >> >> > >> > >>>
> >> >> > >> > >>> ----- Original Message -----
> >> >> > >> > >>> > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com
>
> >> >> > >> > >>> > To: "Dan Tenenbaum" < dtenenba@fhcrc.org >
> >> >> > >> > >>> > Cc: "Bioconductor mailing list" <
> >> >> > >> > >>> > bioconductor@r-project.org >,
> >> >> > >> > >>> > lcollado@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@fhcrc.org >
> >> >> > >> > >>> > wrote:
> >> >> > >> > >>> >
> >> >> > >> > >>> >
> >> >> > >> > >>> >
> >> >> > >> > >>> > Hi Tengfei,
> >> >> > >> > >>> >
> >> >> > >> > >>> > ----- Original Message -----
> >> >> > >> > >>> > > From: "Tengfei Yin" <
tengfei.yin@sbgenomics.com >
> >> >> > >> > >>> >
> >> >> > >> > >>> > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org >
> >> >> > >> > >>> > > Cc: "Bioconductor mailing list" <
> >> >> > > bioconductor@r-project.org
> >> >> > >> > >>> > > >,
> >> >> > >> > >>> > > lcollado@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@fhcrc.org
> >> >> > >> > >>> > > >
> >> >> > >> > >>> > > wrote:
> >> >> > >> > >>> > >
> >> >> > >> > >>> > >
> >> >> > >> > >>> > >
> >> >> > >> > >>> > >
> >> >> > >> > >>> > >
> >> >> > >> > >>> > > ----- Original Message -----
> >> >> > >> > >>> > > > From: "Tengfei Yin" <
tengfei.yin@sbgenomics.com >
> >> >> > >> > >>> > >
> >> >> > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org >
> >> >> > >> > >>> > > > Cc: "Bioconductor mailing list" <
> >> >> > >> > >>> > > > bioconductor@r-project.org >,
> >> >> > >> > >>> > > > lcollado@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@fhcrc.org
> >> >> > >> > >>> > > > > wrote:
> >> >> > >> > >>> > > >
> >> >> > >> > >>> > > >
> >> >> > >> > >>> > > > Hi Tengfei,
> >> >> > >> > >>> > > >
> >> >> > >> > >>> > > >
> >> >> > >> > >>> > > > ----- Original Message -----
> >> >> > >> > >>> > > > > From: "Tengfei Yin" <
tengfei.yin@sbgenomics.com>
> >> >> > >> > >>> > > > > To: lcollado@jhu.edu
> >> >> > >> > >>> > > > > Cc: bioconductor@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@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@jhsph.edu > wrote:
> >> >> > >> > >>> > > > > >
> >> >> > >> > >>> > > > > >> Hello Tengfei + bioc list,
> >> >> > >> > >>> > > > > >>
> >> >> > >> > >>> > > > > >> From
> >> >> > >> > >>> > > > > >>
> >> >> > >> > >>> > > > > >>
> >> >> > >>
> >> >> > >
> >> >> > >
>
http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in
st/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@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@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
[[alternative HTML version deleted]]
