ggbio error: Objects of type OrganismDb not supported by autoplot

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Georg Otto ▴ 120

@georg-otto-6333

Last seen 6.0 years ago

United Kingdom

Dear all, I have a problem reproducing the vignette of the ggbio package: > library(ggbio) > library(Homo.sapiens) > class(Homo.sapiens) [1] "OrganismDb" attr(,"package") [1] "OrganismDbi" > data(genesymbol, package = "biovizBase") > wh <- genesymbol[c("BRCA1", "NBR1")] > wh <- range (wh, ignore.strand = TRUE) > p.txdb <- autoplot(Homo.sapiens, which = wh) Error: Objects of type OrganismDb not supported by autoplot. Please use qplot() or ggplot() instead. Can anybody tell me what is going on? Best wishes, Georg > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Homo.sapiens_1.1.2 [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 [3] org.Hs.eg.db_2.10.1 [4] GO.db_2.10.1 [5] RSQLite_0.11.4 [6] DBI_0.2-7 [7] OrganismDbi_1.4.0 [8] GenomicFeatures_1.14.5 [9] AnnotationDbi_1.24.0 [10] Biobase_2.22.0 [11] ggbio_1.10.16 [12] ggplot2_1.0.0 [13] plyr_1.8.1 [14] Rsamtools_1.14.3 [15] Biostrings_2.30.1 [16] GenomicRanges_1.14.4 [17] XVector_0.2.0 [18] IRanges_1.20.7 [19] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 biovizBase_1.10.8 bitops_1.0-6 [4] BSgenome_1.30.0 cluster_1.15.2 colorspace_1.2-4 [7] compiler_3.0.1 dichromat_2.0-0 digest_0.6.4 [10] Formula_1.1-2 graph_1.40.1 grid_3.0.1 [13] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 [16] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 [19] munsell_0.4.2 proto_0.3-10 RBGL_1.38.0 [22] RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.3 [25] reshape2_1.4 rtracklayer_1.22.7 scales_0.2.4 [28] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 [31] survival_2.37-7 tools_3.0.1 VariantAnnotation_1.8.13 [34] XML_3.98-1.1 zlibbioc_1.8.0 -- Georg Otto The Weatherall Institute of Molecular Medicine Oxford, UK

GO OrganismDb ggbio GO OrganismDb ggbio • 2.7k views

ADD COMMENT • link updated 10.0 years ago by dalloliogm ▴ 50 • written 10.3 years ago by Georg Otto ▴ 120

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dalloliogm ▴ 50

@dalloliogm-7141

Last seen 3.6 years ago

European Union

You must have loaded the package "ggplot2", which also contains a function called autoplot, so the ggbio functions got overwritten.

To make sure that everything works properly, use ggbio::autoplot instead of autoplot.

ADD COMMENT • link 10.0 years ago dalloliogm ▴ 50

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 1 hour ago

United States

Hi Georg, Update to the current version of R and ggbio: > autoplot(Homo.sapiens, which = wh) Error: Objects of type OrganismDb not supported by autoplot. Please use qplot() or ggplot() instead. > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) <snip> But with the current versions: > autoplot(Homo.sapiens, which = wh) Parsing transcripts... Parsing exons... Parsing cds... Parsing utrs... ------exons... ------cdss... ------introns... ------utr... aggregating... Done "gap" is not matching to following arbitrary model terms"cds CDS Cds exon EXON Exon utr UTR Utr" Constructing graphics... Warning message: Removed 2 rows containing missing values (geom_text). > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) Best, Jim On Thu, Aug 21, 2014 at 11:05 AM, Georg Otto <georg.otto at="" imm.ox.ac.uk=""> wrote: > Dear all, > > I have a problem reproducing the vignette of the ggbio package: > > > library(ggbio) > > library(Homo.sapiens) > > class(Homo.sapiens) > [1] "OrganismDb" > attr(,"package") > [1] "OrganismDbi" > > data(genesymbol, package = "biovizBase") > > wh <- genesymbol[c("BRCA1", "NBR1")] > > wh <- range (wh, ignore.strand = TRUE) > > p.txdb <- autoplot(Homo.sapiens, which = wh) > Error: Objects of type OrganismDb not supported by autoplot. Please use > qplot() or ggplot() instead. > > Can anybody tell me what is going on? > > Best wishes, > > Georg > > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Homo.sapiens_1.1.2 > [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 > [3] org.Hs.eg.db_2.10.1 > [4] GO.db_2.10.1 > [5] RSQLite_0.11.4 > [6] DBI_0.2-7 > [7] OrganismDbi_1.4.0 > [8] GenomicFeatures_1.14.5 > [9] AnnotationDbi_1.24.0 > [10] Biobase_2.22.0 > [11] ggbio_1.10.16 > [12] ggplot2_1.0.0 > [13] plyr_1.8.1 > [14] Rsamtools_1.14.3 > [15] Biostrings_2.30.1 > [16] GenomicRanges_1.14.4 > [17] XVector_0.2.0 > [18] IRanges_1.20.7 > [19] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.18.0 biovizBase_1.10.8 bitops_1.0-6 > [4] BSgenome_1.30.0 cluster_1.15.2 colorspace_1.2-4 > [7] compiler_3.0.1 dichromat_2.0-0 digest_0.6.4 > [10] Formula_1.1-2 graph_1.40.1 grid_3.0.1 > [13] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 > [16] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 > [19] munsell_0.4.2 proto_0.3-10 RBGL_1.38.0 > [22] RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.3 > [25] reshape2_1.4 rtracklayer_1.22.7 scales_0.2.4 > [28] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 > [31] survival_2.37-7 tools_3.0.1 > VariantAnnotation_1.8.13 > [34] XML_3.98-1.1 zlibbioc_1.8.0 > > > -- > Georg Otto > The Weatherall Institute of Molecular Medicine > Oxford, UK > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]

ADD COMMENT • link 10.3 years ago James W. MacDonald 67k

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Hey Jim, Thanks for your reply! Warning is fine, I removed the warning in the new version, it's just internally there is a "gap" in the type column as a byproduct; but in practice, you can you specify exons, cds, utr, the introns will be inferred, so no need for 'gap' type. Hey Georg So sorry for the late response Georg, I think like Jim point out, the latest version will fix the problem. cheers Tengfei On Fri, Aug 22, 2014 at 10:05 AM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > Hi Georg, > > Update to the current version of R and ggbio: > > > autoplot(Homo.sapiens, which = wh) > Error: Objects of type OrganismDb not supported by autoplot. Please use > qplot() or ggplot() instead. > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > <snip> > > But with the current versions: > > > autoplot(Homo.sapiens, which = wh) > Parsing transcripts... > Parsing exons... > Parsing cds... > Parsing utrs... > ------exons... > ------cdss... > ------introns... > ------utr... > aggregating... > Done > "gap" is not matching to following arbitrary model terms"cds CDS Cds exon > EXON Exon utr UTR Utr" > Constructing graphics... > Warning message: > Removed 2 rows containing missing values (geom_text). > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-unknown-linux-gnu (64-bit) > > Best, > > Jim > > > > > > On Thu, Aug 21, 2014 at 11:05 AM, Georg Otto <georg.otto at="" imm.ox.ac.uk=""> > wrote: > > > Dear all, > > > > I have a problem reproducing the vignette of the ggbio package: > > > > > library(ggbio) > > > library(Homo.sapiens) > > > class(Homo.sapiens) > > [1] "OrganismDb" > > attr(,"package") > > [1] "OrganismDbi" > > > data(genesymbol, package = "biovizBase") > > > wh <- genesymbol[c("BRCA1", "NBR1")] > > > wh <- range (wh, ignore.strand = TRUE) > > > p.txdb <- autoplot(Homo.sapiens, which = wh) > > Error: Objects of type OrganismDb not supported by autoplot. Please use > > qplot() or ggplot() instead. > > > > Can anybody tell me what is going on? > > > > Best wishes, > > > > Georg > > > > > sessionInfo() > > R version 3.0.1 (2013-05-16) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] Homo.sapiens_1.1.2 > > [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 > > [3] org.Hs.eg.db_2.10.1 > > [4] GO.db_2.10.1 > > [5] RSQLite_0.11.4 > > [6] DBI_0.2-7 > > [7] OrganismDbi_1.4.0 > > [8] GenomicFeatures_1.14.5 > > [9] AnnotationDbi_1.24.0 > > [10] Biobase_2.22.0 > > [11] ggbio_1.10.16 > > [12] ggplot2_1.0.0 > > [13] plyr_1.8.1 > > [14] Rsamtools_1.14.3 > > [15] Biostrings_2.30.1 > > [16] GenomicRanges_1.14.4 > > [17] XVector_0.2.0 > > [18] IRanges_1.20.7 > > [19] BiocGenerics_0.8.0 > > > > loaded via a namespace (and not attached): > > [1] biomaRt_2.18.0 biovizBase_1.10.8 bitops_1.0-6 > > [4] BSgenome_1.30.0 cluster_1.15.2 colorspace_1.2-4 > > [7] compiler_3.0.1 dichromat_2.0-0 digest_0.6.4 > > [10] Formula_1.1-2 graph_1.40.1 grid_3.0.1 > > [13] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 > > [16] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 > > [19] munsell_0.4.2 proto_0.3-10 RBGL_1.38.0 > > [22] RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.3 > > [25] reshape2_1.4 rtracklayer_1.22.7 scales_0.2.4 > > [28] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 > > [31] survival_2.37-7 tools_3.0.1 > > VariantAnnotation_1.8.13 > > [34] XML_3.98-1.1 zlibbioc_1.8.0 > > > > > > -- > > Georg Otto > > The Weatherall Institute of Molecular Medicine > > Oxford, UK > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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 Product Manager Seven Bridges Genomics sbgenomics.com One Broadway FL 7 Cambridge, MA 02142 (617) 866-0446 [[alternative HTML version deleted]]

ADD REPLY • link 10.2 years ago Tengfei Yin ▴ 490

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