[BioC] ggbio 1.12.0 autoplot() with txdb example is broken
Dan Tenenbaum
dtenenba at fhcrc.org
Wed Apr 23 22:03:23 CEST 2014
----- Original Message -----
> From: "Leonardo Collado Torres" <lcollado at jhsph.edu>
> To: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
> Cc: bioconductor at r-project.org
> Sent: Wednesday, April 23, 2014 12:58:37 PM
> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
>
> See the email below. I forgot to send it with my registered email for
> the BioC list.
>
> On Wed, Apr 23, 2014 at 3:45 PM, Leonardo Collado Torres
> <lcollado at jhu.edu> wrote:
> > Awesome, thank you Tengfei!
> >
> > Also, Dan, your https://github.com/dtenenba/renv/blob/master/renv
> > script looks interesting. I'm curious if what you described of
> > installing a new R version and creating a symlink (like from
> > R.framework.bioc214_snowleopard to R.framework) works with Rswitch.
It's meant to be a replacement for Rswitch. I think Rswitch does things in a different way.
So you'd need to pick either 'renv' or Rswitch and stick with it.
But I'm not sure if Rswitch will let you install two identical copies of R. One would have to experiment...
> > I'm not an emacs user, so Rswitch has been working pretty well for
> > me.
If Rswitch is working for you, I'd suggest sticking with it.
My script was motivated by the fact that I have many copies of R on my machine and needed a way to manage them, and that I find it quicker to do things from the command line.
Dan
> > Yet this is the first time that I need two R installations from the
> > same version (thanks for the trick suggestion!): basically I've
> > been
> > using my own `derfinder` package but I want to test it for
> > submitting
> > it to Bioc.
> >
> > Cheers,
> > Leo
> >
> >
> >
> > On Wed, Apr 23, 2014 at 3:35 PM, Tengfei Yin
> > <tengfei.yin at sbgenomics.com> wrote:
> >> Hi
> >>
> >> I just fixed the bug in bioc 2.14 and checked in the fix, fixed in
> >> biovizbase 1.12.1 and ggbio 1.12.2, please update later and let me
> >> know if
> >> that doesn't work.
> >>
> >> Because in biovizBase, I am using ignore.strand in the wrong
> >> function
> >> ranges,GRangesList, sorry about this.
> >>
> >> thanks
> >>
> >> 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
>
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