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

Leonardo Collado Torres lcollado at jhsph.edu
Wed Apr 23 21:58:37 CEST 2014


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.
> I'm not an emacs user, so Rswitch has been working pretty well for me.
> 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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