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Question: Problems with ggbio
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gravatar for Michael Muratet
5.4 years ago by
Michael Muratet420 wrote:
Greetings I installed a development version of bioconductor to get the distanceToNearest functionality (sessionInfo below). I am trying to plot a GRanges object with ggbio > is(hits) [1] "GRanges" "GenomicRanges" "Vector" "GenomicRangesORmissing" "GenomicRangesORGRangesList" [6] "RangedDataORGenomicRanges" "Annotated" > p <- qplot(hits) > print(p) Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class 'structure("GRanges", package = "GenomicRanges")' into a data.frame I haven't been able to track down the problem. Have I created a compatibility issue with the development version? Is it operator error? I could save the object and go back to release versions. Thanks for the help Mike > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (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] ggbio_1.5.6 ggplot2_0.9.1 BiocInstaller_1.5.11 rtracklayer_1.17.11 GenomicFeatures_1.9.19 AnnotationDbi_1.19.16 [7] Biobase_2.17.6 GenomicRanges_1.9.29 IRanges_1.15.17 BiocGenerics_0.3.0 loaded via a namespace (and not attached): [1] biomaRt_2.13.1 Biostrings_2.25.6 biovizBase_1.5.2 bitops_1.0-4.1 BSgenome_1.25.3 cluster_1.14.2 [7] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 grid_2.15.0 gridExtra_0.9 [13] Hmisc_3.9-3 labeling_0.1 lattice_0.20-6 MASS_7.3-19 Matrix_1.0-6 memoise_0.1 [19] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 reshape2_1.2.1 [25] Rsamtools_1.9.19 RSQLite_0.11.1 scales_0.2.1 snpStats_1.7.2 splines_2.15.0 stats4_2.15.0 [31] stringr_0.6 survival_2.36-14 tools_2.15.0 VariantAnnotation_1.3.16 XML_3.9-4 zlibbioc_1.3.0 Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806
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ADD COMMENTlink modified 5.4 years ago by Michael Lawrence9.8k • written 5.4 years ago by Michael Muratet420
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gravatar for Michael Lawrence
5.4 years ago by
United States
Michael Lawrence9.8k wrote:
Hi Michael, The qplot generic has been replaced with "autoplot". On Fri, Jul 6, 2012 at 10:44 AM, Michael Muratet <mmuratet@hudsonalpha.org>wrote: > Greetings > > I installed a development version of bioconductor to get the > distanceToNearest functionality (sessionInfo below). I am trying to plot a > GRanges object with ggbio > > > is(hits) > [1] "GRanges" "GenomicRanges" "Vector" > "GenomicRangesORmissing" "GenomicRangesORGRangesList" > [6] "RangedDataORGenomicRanges" "Annotated" > > > p <- qplot(hits) > > print(p) > Error in as.data.frame.default(x[[i]], optional = TRUE) : > cannot coerce class 'structure("GRanges", package = "GenomicRanges")' > into a data.frame > > I haven't been able to track down the problem. Have I created a > compatibility issue with the development version? Is it operator error? I > could save the object and go back to release versions. > > Thanks for the help > > Mike > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_**64 (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] ggbio_1.5.6 ggplot2_0.9.1 BiocInstaller_1.5.11 > rtracklayer_1.17.11 GenomicFeatures_1.9.19 AnnotationDbi_1.19.16 > [7] Biobase_2.17.6 GenomicRanges_1.9.29 IRanges_1.15.17 > BiocGenerics_0.3.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.13.1 Biostrings_2.25.6 biovizBase_1.5.2 > bitops_1.0-4.1 BSgenome_1.25.3 cluster_1.14.2 > [7] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 > digest_0.5.2 grid_2.15.0 gridExtra_0.9 > [13] Hmisc_3.9-3 labeling_0.1 lattice_0.20-6 > MASS_7.3-19 Matrix_1.0-6 memoise_0.1 > [19] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 > RColorBrewer_1.0-5 RCurl_1.91-1 reshape2_1.2.1 > [25] Rsamtools_1.9.19 RSQLite_0.11.1 scales_0.2.1 > snpStats_1.7.2 splines_2.15.0 stats4_2.15.0 > [31] stringr_0.6 survival_2.36-14 tools_2.15.0 > VariantAnnotation_1.3.16 XML_3.9-4 zlibbioc_1.3.0 > > > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > mmuratet@hudsonalpha.org > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.4 years ago by Michael Lawrence9.8k
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