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lawremi / ggbio

Grid and ggplot2 based visualization for biological data
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ggbio::plotIdeogram() not working on R 3.0.2 #45

Closed lcolladotor closed 10 years ago

lcolladotor commented 10 years ago

I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 that I think is related to changes in R. The error can also be seen in http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf (search 'unnamed' on the pdf).

Below is the error from running the example code for plotIdeogram.

library(ggbio)
library(biovizBase)
data(hg19IdeogramCyto, package = "biovizBase")
biovizBase::isIdeogram(hg19IdeogramCyto)  return TRUE
plotIdeogram(hg19IdeogramCyto, "chr1")

Error in initialize(value, ...) : unnamed argument must extend either the S3 class or the class of the data part; not true of class “GGbio”

traceback()

6: stop(gettextf("unnamed argument must extend either the S3 class or the class of the data part; not true of class %s", dQuote(Classi)), domain = NA) 5: initialize(value, ...) 4: initialize(value, ...) 3: new("Ideogram", x) 2: Ideogram(p) 1: plotIdeogram(hg19IdeogramCyto, "chr1")

sessionInfo()

R version 3.0.2 (2013-09-25) 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] stats graphics grDevices utils datasets methods base

other attached packages: [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1

loaded via a namespace (and not attached): [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0
[6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7
[11] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2
[16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 IRanges_1.20.4 labeling_0.2
[21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 plyr_1.8
[26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3
[31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2
[36] stringr_0.6.2 tools_3.0.2 VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0
[41] zlibbioc_1.8.0

Thank you, Leonardo

Posted to https://stat.ethz.ch/pipermail/bioconductor/2013-November/055843.html (see T. Yin's reply there) and posting here for completeness.

lcolladotor commented 10 years ago

As stated in https://stat.ethz.ch/pipermail/bioconductor/2013-November/056150.html this should be fixed in ggbio 1.10.8

Will close once I can check with that version.

lcolladotor commented 10 years ago

Tested and it works now on ggbio 1.10.8