[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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