[Bioc-devel] loading VariantAnnotation package breaks ggplot2::qplot when faceting, potential cbind problem?

On Wed, Sep 12, 2012 at 5:09 PM, Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>> wrote:

    On 9/12/2012 1:47 PM, Tengfei Yin wrote:

    Dear developers,

    I hit some problem I am not able to fix or find what's really going on.
    When I simply import VCF class in namespace, that will break ggplot2::qplot
    function when faceting turns on, at first I thought it's ggbio's problem,
    but when I dig into it, looks like, the cbind function used inside ggplot2
    changed, looks like ggplot2 suppose to use base::cbind, but use
    methods:::cbind after loading VariantAnnotation. But maybe I am digging in
    the wrong direction.

    Following code demonstrate when loading VariantAnnotation, ggplot2 cannot
    faceting, even though I import only VCF class  in a minimal package, and
    make the package depends on methods and ggplot2(0.9.2), the same issue
    still exists, not sure if I am posting in the right place or not.  Please
    let me know if I should post this in somewhere else, thanks.

    library(ggplot2)
    qplot(x = mpg, y = cyl, data = mtcars, facets = . ~ cyl)
    library(VariantAnnotation)

    Loading required package: GenomicRanges
    Loading required package: BiocGenerics

    Attaching package: ?BiocGenerics?

    The following object(s) are masked from ?package:stats?:

         xtabs

    The following object(s) are masked from ?package:base?:

         anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
         get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
         pmax.int  <http://pmax.int>, pmin,pmin.int  <http://pmin.int>, Position, rbind, Reduce,rep.int  <http://rep.int>,
         rownames, sapply, setdiff, table, tapply, union, unique

    Loading required package: IRanges
    Loading required package: Rsamtools
    Loading required package: Biostrings

    qplot(x = mpg, y = cyl, data = mtcars, facets = . ~ cyl)

    Error inrep.int  <http://rep.int>("", ncol(r)) : incorrect type for second argument

    Wow this is baroque. A simplification of the problem is

     > base::cbind

    function (..., deparse.level = 1)
    .Internal(cbind(deparse.level, ...))
    <environment: namespace:base>

     > library(snpStats)
     > head(base::cbind)

    1 function (..., deparse.level = 1)
    2 {
    3     na <- nargs() - (!missing(deparse.level))
    4     deparse.level <- as.integer(deparse.level)
    5     stopifnot(0 <= deparse.level, deparse.level <= 2)
    6     argl <- list(...)

    snpStats (which VariantAnnotation Imports:) uses 'cbind2' and
    methods:::bind_activation. bind_activation changes the definition of
    cbind. I think this is a left-over from a time when methods could
    not be written on ... . I'll try and get some clarification from
    R-devel.


Hi Martin,

Thanks a lot for the quick reply and the clarification, by the way, is
there any workaround for this release of Bioconductor, if I want to
import VariantAnnotation and at the same time use ggplot2 as usual?

Thanks

Tengfei


    Martin

    sessionInfo()

    R version 2.15.1 (2012-06-22)
    Platform: x86_64-pc-linux-gnu (64-bit)

    locale:
      [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
      [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
      [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
      [7] LC_PAPER=C                 LC_NAME=C
      [9] LC_ADDRESS=C               LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods   base

    other attached packages:
    [1] ggplot2_0.9.2            VariantAnnotation_1.3.18 Rsamtools_1.9.26

    [4] Biostrings_2.25.10       GenomicRanges_1.9.47     IRanges_1.15.34

    [7] BiocGenerics_0.3.1

    loaded via a namespace (and not attached):
      [1] AnnotationDbi_1.19.28  Biobase_2.17.6         biomaRt_2.13.2
      [4] bitops_1.0-4.1         BSgenome_1.25.6        colorspace_1.1-1
      [7] DBI_0.2-5              dichromat_1.2-4        digest_0.5.1
    [10] GenomicFeatures_1.9.29 grid_2.15.1            gtable_0.1.1
    [13] labeling_0.1           lattice_0.20-6         MASS_7.3-20
    [16] Matrix_1.0-6           memoise_0.1            munsell_0.3
    [19] plyr_1.7.1             proto_0.3-9.2          RColorBrewer_1.0-5
    [22] RCurl_1.91-1           reshape2_1.2.1         RSQLite_0.11.1
    [25] rtracklayer_1.17.17    scales_0.2.2           snpStats_1.7.3
    [28] splines_2.15.1         stats4_2.15.1          stringr_0.6.1
    [31] survival_2.36-14       tools_2.15.1           XML_3.9-4
    [34] zlibbioc_1.3.0
    Thanks a lot

    Tengfei

    --
    Dr. Martin Morgan, PhD
    Fred Hutchinson Cancer Research Center
    1100 Fairview Ave. N.
    PO Box 19024 Seattle, WA 98109




--
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274