Michael, Thanks for the diagnosis. I'm not up on namespaces in R or I would offer to patch. Meantime, I wonder if there is a workaround.... Guessing, I tried namespaceImport(asNamespace('GGally'),from=asNamespace('ggplot2')) but no dice. Thanks, Malcolm From: Michael Lawrence [mailto:lawrence.michael@gene.com] Sent: Saturday, November 09, 2013 11:38 AM To: Paulson, Ariel Cc: Cook, Malcolm; r-discussion@listserv.stowers.org; bioconductor@r-project.org; Tengfei Yin (tengfei.yin@sbgenomics.com); schloerke@gmail.com Subject: Re: [BioC] GGally ggbio conflict/bug Couple of problems: GGally: needs to import(ggplot2) ggbio: its GGbio object should support $<- (i.e., it should pass through to its ggplot slot) If either one is fixed, the problem is resolved. But both should be. Maintainers: ready, set, fix! ;) Michael On Fri, Nov 8, 2013 at 3:40 PM, Paulson, Ariel <apa@stowers.org<mailto:apa@stowers.org>> wrote: Library load order does not affect the phenotype? -----Original Message----- From: r-discussion-bounces@listserv.stowers.org<mailto:r-discussion- bounces@listserv.stowers.org=""> [mailto:r-discussion- bounces@listserv.stowers.org<mailto:r-discussion- bounces@listserv.stowers.org="">] On Behalf Of Cook, Malcolm Sent: Friday, November 08, 2013 5:09 PM To: 'r-discussion@listserv.stowers.org<mailto:r-discussion@listserv.st owers.org="">'; 'bioconductor@r-project.org<mailto:bioconductor@r-project.org>'; 'Tengfei Yin (tengfei.yin@sbgenomics.com<mailto:tengfei.yin@sbgenomics.com>)'; 'schloerke@gmail.com<mailto:schloerke@gmail.com>' Subject: [R-discussion] GGally ggbio conflict/bug H'lo fellow and prospective users of R libraries GGally/ggbio, both stupendous extensions to the ggplot library, I have an unfortunate interaction to report.... In my hands, loading ggbio on top of GGally causes GGally examples to fail. look see: > library(GGally) Loading required package: ggplot2 Loading required package: reshape Loading required package: plyr Attaching package: 'reshape' The following objects are masked from 'package:plyr': rename, round_any Warning messages: 1: replacing previous import by 'reshape::rename' when loading 'GGally' 2: replacing previous import by 'reshape::round_any' when loading 'GGally' >example(ggpairs) # output excised ... >pm # the plot is pretty # now load the other library: >library(ggbio) The following objects are masked from 'package:ggplot2': geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, xlim > pm # but now I don't get to see the plot because: Error in `$<-`(`*tmp*`, "type", value = "diag") : no method for assigning subsets of this S4 class > My workaround is ... erhm ...egad ... ... don't use ggbio, which, due to other issues with current release (reported seperatlely) I have most unfortunately stopped using anyway. Thanks! What else? ~Malcolm Cook PS. oh, yeah: sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] ggbio_1.10.0 GGally_0.4.4 reshape_0.8.4 plyr_1.8 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 biovizBase_1.10.0 bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 IRanges_1.20.4 labeling_0.2 lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 [25] parallel_3.0.2 proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 stringr_0.6.2 tools_3.0.2 VariantAnnotation_1.8.2 XML_3.98-1.1 XVector_0.2.0 zlibbioc_1.8.0 > _______________________________________________ r-discussion mailing list r-discussion@listserv.stowers.org<mailto:r-discussion@listserv.stowers .org=""> http://listserv.stowers.org/mailman/listinfo/r-discussion _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Hi Sorry for the late fix. I just fixed it in release branch 1.10.4 ggbio, please update two days later. 1. As Michael suggested, I support $<- and $ for GGbio class 2. But it's more complicated, I override stat_bin and other existing method, and to avoid using proto structure, I use a hack in ggbio, which wrap a call to "+" method for later evaluation which inject the raw data and do transformation, but this conflict with some behavior in ggplot2, so I change the method to behave differently for GGbio + or ggplot + method, and also re-write ggplot generic function, only produce GGbio object when it's not a traditional object for ggplot2. I will update devel branch later soon. cheers Tengfei On Sat, Nov 9, 2013 at 12:37 PM, Michael Lawrence <lawrence.michael@gene.com> wrote: > Couple of problems: > > GGally: needs to import(ggplot2) > ggbio: its GGbio object should support $<- (i.e., it should pass through > to its ggplot slot) > > If either one is fixed, the problem is resolved. But both should be. > > Maintainers: ready, set, fix! ;) > > Michael > > > On Fri, Nov 8, 2013 at 3:40 PM, Paulson, Ariel <apa@stowers.org> wrote: > >> Library load order does not affect the phenotype? >> >> -----Original Message----- >> From: r-discussion-bounces@listserv.stowers.org [mailto: >> r-discussion-bounces@listserv.stowers.org] On Behalf Of Cook, Malcolm >> Sent: Friday, November 08, 2013 5:09 PM >> To: 'r-discussion@listserv.stowers.org'; 'bioconductor@r-project.org'; >> 'Tengfei Yin (tengfei.yin@sbgenomics.com)'; 'schloerke@gmail.com' >> Subject: [R-discussion] GGally ggbio conflict/bug >> >> H'lo fellow and prospective users of R libraries GGally/ggbio, both >> stupendous extensions to the ggplot library, >> >> I have an unfortunate interaction to report.... >> >> In my hands, loading ggbio on top of GGally causes GGally examples to >> fail. >> >> look see: >> >> > library(GGally) >> Loading required package: ggplot2 >> Loading required package: reshape >> Loading required package: plyr >> >> Attaching package: 'reshape' >> >> The following objects are masked from 'package:plyr': >> >> rename, round_any >> >> Warning messages: >> 1: replacing previous import by 'reshape::rename' when loading 'GGally' >> 2: replacing previous import by 'reshape::round_any' when loading 'GGally' >> >> >example(ggpairs) >> # output excised ... >> >pm # the plot is pretty >> >> # now load the other library: >> >library(ggbio) >> >> The following objects are masked from 'package:ggplot2': >> >> geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, >> xlim >> >> > pm # but now I don't get to see the plot because: >> Error in `$<-`(`*tmp*`, "type", value = "diag") : >> no method for assigning subsets of this S4 class >> > >> >> My workaround is ... erhm ...egad ... >> >> ... don't use ggbio, which, due to other issues with current release >> (reported seperatlely) I have most unfortunately stopped using anyway. >> >> Thanks! >> >> What else? >> >> ~Malcolm Cook >> >> >> PS. oh, yeah: >> >> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 >> LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C >> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] ggbio_1.10.0 GGally_0.4.4 reshape_0.8.4 plyr_1.8 >> 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 biovizBase_1.10.0 >> bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >> colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >> digest_0.6.3 GenomicFeatures_1.14.0 GenomicRanges_1.14.3 >> grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 >> Hmisc_3.12-2 IRanges_1.20.4 labeling_0.2 >> lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >> [25] parallel_3.0.2 proto_0.3-10 RColorBrewer_1.0-5 >> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >> Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 >> scales_0.2.3 stats4_3.0.2 stringr_0.6.2 >> tools_3.0.2 VariantAnnotation_1.8.2 XML_3.98-1.1 >> XVector_0.2.0 zlibbioc_1.8.0 >> > >> >> _______________________________________________ >> r-discussion mailing list >> r-discussion@listserv.stowers.org >> http://listserv.stowers.org/mailman/listinfo/r-discussion >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]