Question

tracks() and plotIdeogram() with non desired results in ggbio 1.10.9

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Leonardo Collado Torres ★ 1.1k

@lcolladotor

Last seen 5 weeks ago

United States

Hello Tengfei and BioC list, I believe that tracks() and plotIdeogram() are not working as intended in ggbio 1.10.9 Page 20 of http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst /doc/ggbio.pdf shows a tracks example plot with an ideogram. I think that tracks() is not handling properly the ggplot2 controls for the ideogram track as it is adding what looks like a layer label ("chr1" in grey) and a discrete scale (probably scale_fill_discrete) for the cytobands. You can produce the plot using the code in pages 19 and 20 from the vignette (pasted below): > library(ggbio) > ## require internet connection > p.ideo <- plotIdeogram(genome = "hg19") Loading... Done use chr1 automatically > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > wh <- GRanges("chr16", IRanges(30064491, 30081734)) > p1 <- autoplot(txdb, which = wh, names.expr = "gene_id") Aggregating TranscriptDb... Parsing exons... Parsing cds... Parsing transcripts... Parsing utrs... ------exons... ------cdss... ------introns... ------utr... aggregating... Done Constructing graphics... Warning message: In ans[] <- x : number of items to replace is not a multiple of replacement length > p2 <- autoplot(txdb, which = wh, stat = "reduce", color = "brown", + fill = "brown") Aggregating TranscriptDb... Parsing exons... Parsing cds... Parsing transcripts... Parsing utrs... ------exons... ------cdss... ------introns... ------utr... aggregating... Done Constructing graphics... Warning message: In ans[] <- x : number of items to replace is not a multiple of replacement length > tracks(p.ideo, full = p1, reduce = p2, heights = c(1.5, 5, 1)) + + ylab("") + theme_tracks_sunset() I noticed this when using: > library(derfinder) ## From https://github.com/lcolladotor/derfinder > example("plotCluster", "derfinder") Session info: > 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] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] bumphunter_1.3.3 locfit_1.5-9.1 iterators_1.0.6 [4] foreach_1.4.1 derfinder_0.0.37 RcppArmadillo_0.3.920.3 [7] Rcpp_0.10.6 TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.14.2 [10] AnnotationDbi_1.24.0 Biobase_2.22.0 rtracklayer_1.22.0 [13] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.6 [16] BiocGenerics_0.8.0 ggbio_1.10.9 ggplot2_0.9.3.1 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 Biostrings_2.30.1 biovizBase_1.10.4 bitops_1.0-6 BSgenome_1.30.0 [6] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 [11] digest_0.6.3 doRNG_1.5.5 Formula_1.1-1 grid_3.0.2 gridExtra_0.9.1 [16] gtable_0.1.2 Hmisc_3.13-0 itertools_0.1-1 labeling_0.2 lattice_0.20-24 [21] MASS_7.3-29 matrixStats_0.8.12 munsell_0.4.2 pkgmaker_0.17.4 plyr_1.8 [26] proto_0.3-10 qvalue_1.36.0 R.methodsS3_1.5.2 RColorBrewer_1.0-5 RCurl_1.95-4.1 [31] registry_0.2 reshape2_1.2.2 rngtools_1.2.3 Rsamtools_1.14.2 RSQLite_0.11.4 [36] scales_0.2.3 splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-4 [41] tcltk_3.0.2 tools_3.0.2 VariantAnnotation_1.8.6 XML_3.95-0.2 xtable_1.7-1 [46] zlibbioc_1.8.0 Best, Leonardo Leonardo Collado Torres, PhD student Department of Biostatistics Johns Hopkins University Bloomberg School of Public Health Website: http://www.biostat.jhsph.edu/~lcollado/<http: bit.ly="" lcolladotorres=""> Blog: http://lcolladotor.github.io/ <http: bit.ly="" fellbit=""> [[alternative HTML version deleted]]

TranscriptDb ideogram TranscriptDb ideogram • 1.6k views

ADD COMMENT • link updated 11.0 years ago by Tengfei Yin ▴ 490 • written 11.0 years ago by Leonardo Collado Torres ★ 1.1k

score 0 · Answer 1 · 2013-11-25

Thanks for reporting the issue, it's clearly another bug, I will work on that today! cheers Tengfei On Mon, Nov 25, 2013 at 2:20 PM, Leonardo Collado Torres <lcollado@jhsph.edu> wrote: > Hello Tengfei and BioC list, > > I believe that tracks() and plotIdeogram() are not working as intended in > ggbio 1.10.9 Page 20 of > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf shows > a tracks example plot with an ideogram. I think that tracks() is not > handling properly the ggplot2 controls for the ideogram track as it is > adding what looks like a layer label ("chr1" in grey) and a discrete scale > (probably scale_fill_discrete) for the cytobands. > > You can produce the plot using the code in pages 19 and 20 from the > vignette (pasted below): > > > library(ggbio) > > ## require internet connection > > p.ideo <- plotIdeogram(genome = "hg19") > Loading... > Done > use chr1 automatically > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > wh <- GRanges("chr16", IRanges(30064491, 30081734)) > > p1 <- autoplot(txdb, which = wh, names.expr = "gene_id") > Aggregating TranscriptDb... > Parsing exons... > Parsing cds... > Parsing transcripts... > Parsing utrs... > ------exons... > ------cdss... > ------introns... > ------utr... > aggregating... > Done > Constructing graphics... > Warning message: > In ans[] <- x : > number of items to replace is not a multiple of replacement length > > p2 <- autoplot(txdb, which = wh, stat = "reduce", color = "brown", > + fill = "brown") > Aggregating TranscriptDb... > Parsing exons... > Parsing cds... > Parsing transcripts... > Parsing utrs... > ------exons... > ------cdss... > ------introns... > ------utr... > aggregating... > Done > Constructing graphics... > Warning message: > In ans[] <- x : > number of items to replace is not a multiple of replacement length > > tracks(p.ideo, full = p1, reduce = p2, heights = c(1.5, 5, 1)) + > + ylab("") + theme_tracks_sunset() > > I noticed this when using: > > > library(derfinder) ## From https://github.com/lcolladotor/derfinder > > example("plotCluster", "derfinder") > > > Session info: > > > 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] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] bumphunter_1.3.3 locfit_1.5-9.1 > iterators_1.0.6 > [4] foreach_1.4.1 derfinder_0.0.37 > RcppArmadillo_0.3.920.3 > [7] Rcpp_0.10.6 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.14.2 > > [10] AnnotationDbi_1.24.0 Biobase_2.22.0 > rtracklayer_1.22.0 > [13] GenomicRanges_1.14.3 XVector_0.2.0 > IRanges_1.20.6 > [16] BiocGenerics_0.8.0 ggbio_1.10.9 > ggplot2_0.9.3.1 > > loaded via a namespace (and not attached): > [1] biomaRt_2.18.0 Biostrings_2.30.1 biovizBase_1.10.4 > bitops_1.0-6 BSgenome_1.30.0 > [6] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-4 > DBI_0.2-7 dichromat_2.0-0 > [11] digest_0.6.3 doRNG_1.5.5 Formula_1.1-1 > grid_3.0.2 gridExtra_0.9.1 > [16] gtable_0.1.2 Hmisc_3.13-0 itertools_0.1-1 > labeling_0.2 lattice_0.20-24 > [21] MASS_7.3-29 matrixStats_0.8.12 munsell_0.4.2 > pkgmaker_0.17.4 plyr_1.8 > [26] proto_0.3-10 qvalue_1.36.0 R.methodsS3_1.5.2 > RColorBrewer_1.0-5 RCurl_1.95-4.1 > [31] registry_0.2 reshape2_1.2.2 rngtools_1.2.3 > Rsamtools_1.14.2 RSQLite_0.11.4 > [36] scales_0.2.3 splines_3.0.2 stats4_3.0.2 > stringr_0.6.2 survival_2.37-4 > [41] tcltk_3.0.2 tools_3.0.2 > VariantAnnotation_1.8.6 XML_3.95-0.2 xtable_1.7-1 > [46] zlibbioc_1.8.0 > > > Best, > Leonardo > > Leonardo Collado Torres, PhD student > Department of Biostatistics > Johns Hopkins University > Bloomberg School of Public Health > Website: http://www.biostat.jhsph.edu/~lcollado/<http: bit.ly="" lcolladotorres=""> > Blog: http://lcolladotor.github.io/ <http: bit.ly="" fellbit=""> > > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]