[BioC] ggbio 1.12.0 autoplot() with txdb example is broken
Leonardo Collado Torres
lcollado at jhsph.edu
Wed Apr 23 16:51:07 CEST 2014
Hello again,
Looking back, I have a file from 2014-04-15 with ggbio 1.12.0 where
autoplot() with a txdb was working.
The code is not the same from the example I reported above, but it
uses the same ggbio functionality. You can see the working output at
https://rawgit.com/lcolladotor/derfinderReport/master/inst/basicExploration/basicExploration.html#Best_region_clusters
while the R session is at the end of
https://rawgit.com/lcolladotor/derfinderReport/master/inst/basicExploration/basicExploration.html#Details
In particular, the working version used:
* GenomicRanges 1.16.0 instead of 1.16.2
* IRanges 1.22.2 instead of 1.22.3
* GenomeInfoDb 1.0.1 instead of 1.0.2
So, it seems that the problem is indeed related to recent updates to
GenomicRanges (or maybe IRanges, GenomeInfoDb).
On a different topic, there is no equivalent to using
devtools::install_github(ref), right? With it, I can install a version
of a GitHub-hosted package for a specific reference (which can be a
specific commit).
Thanks,
Leonardo
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
>>
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