Question: plotIdeogram for non-human or mouse genome
0
gravatar for Mark Dunning
5.4 years ago by
Mark Dunning1.1k
Sheffield, Uk
Mark Dunning1.1k wrote:
Hi all, I'm trying to plot an ideogram for the "dm3" genome using ggbio. I believe the following should work (it did for previous version of BioC). plotIdeogram(genome = "dm3") However, I get an error. Error in FUN("dm3"[[1L]], ...) : object 'cytobands' not found In the code I can't see where cytobands is defined. How can I get the ideogram for dm3. Regards, Mark Ideogram(obj, xlabel = xlabel, subchr = subchr, aspect.ratio = aspect.ratio, color = color, fill = fill, alpha = alpha, size = size, zoom.region = zoom.region, zoom.offset = zoom.offset, genome = genome) debug: { if (missing(obj)) { data(ideoCyto, package = "biovizBase") if (genome %in% names(ideoCyto)) { obj <- ideoCyto[[genome]] } else { obj <- getIdeogram(genome = genome, subchr = subchr, cytobands = cytobands) > sessionInfo()R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.24.2 GenomicRanges_1.16.2 GenomeInfoDb_1.0.2 IRanges_1.22.4 [5] ggbio_1.12.8 ggplot2_1.0.0 BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.26.0 BatchJobs_1.2 BBmisc_1.6 [4] Biobase_2.24.0 BiocParallel_0.6.0 biomaRt_2.20.0 [7] Biostrings_2.32.1 biovizBase_1.12.1 bitops_1.0-6 [10] brew_1.0-6 BSgenome_1.32.0 cluster_1.15.2 [13] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 [16] dichromat_2.0-0 digest_0.6.4 fail_1.2 [19] foreach_1.4.1 Formula_1.1-1 GenomicAlignments_1.0.0 [22] GenomicFeatures_1.16.0 grid_3.1.0 gridExtra_0.9.1 [25] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.6 [28] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-32 [31] munsell_0.4.2 plyr_1.8.1 proto_0.3-10 [34] RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1 [37] reshape2_1.4 Rsamtools_1.16.0 RSQLite_0.11.4 [40] scales_0.2.4 sendmailR_1.1-2 splines_3.1.0 [43] stats4_3.1.0 stringr_0.6.2 survival_2.37-7 [46] tools_3.1.0 VariantAnnotation_1.10.0 XML_3.98-1.1 [49] XVector_0.4.0 zlibbioc_1.10.0 [[alternative HTML version deleted]]
ideogram ggbio • 1.3k views
ADD COMMENTlink modified 5.3 years ago by Tengfei Yin490 • written 5.4 years ago by Mark Dunning1.1k
Answer: plotIdeogram for non-human or mouse genome
0
gravatar for Tengfei Yin
5.3 years ago by
Tengfei Yin490
Tengfei Yin490 wrote:
Hi Mark Sorry for the late reply, in short, there is a bug for cytoband parameters, I fixed in the released branch biovizBase 1.12.3, and ggbio 1.12.10. But "dm3" doesn't have gieStain value, that's another problem, you have to find it somewhere. Then manually assign the color like something below library(biovizBase) dm3 <- getIdeogram(genome = "dm3") ## but the giestain value is NA > head(dm3) GRanges with 6 ranges and 2 metadata columns: seqnames ranges strand | name gieStain <rle> <iranges> <rle> | <factor> <factor> [1] chr2L [ 1, 22221] * | 21A5 n/a [2] chr2L [ 22221, 98619] * | 21B1 n/a [3] chr2L [ 98619, 134010] * | 21B2 n/a [4] chr2L [134010, 161234] * | 21B3 n/a [5] chr2L [161234, 213130] * | 21B4 n/a [6] chr2L [213130, 256688] * | 21B5 n/a --- seqlengths: chr2L chr2R chr3L chr3R chr4 chrX 23011544 21146708 24543557 27905053 1351857 22422827 ## current supported gieStain names names(biovizBase:::.cytobandColor()) [1] "gneg" "stalk" "acen" "gpos" "gvar" "gpos1" "gpos2" [8] "gpos3" "gpos4" "gpos5" "gpos6" "gpos7" "gpos8" "gpos9" [15] "gpos10" "gpos11" "gpos12" "gpos13" "gpos14" "gpos15" "gpos16" [22] "gpos17" "gpos18" "gpos19" "gpos20" "gpos21" "gpos22" "gpos23" [29] "gpos24" "gpos25" "gpos26" "gpos27" "gpos28" "gpos29" "gpos30" [36] "gpos31" "gpos32" "gpos33" "gpos34" "gpos35" "gpos36" "gpos37" [43] "gpos38" "gpos39" "gpos40" "gpos41" "gpos42" "gpos43" "gpos44" [50] "gpos45" "gpos46" "gpos47" "gpos48" "gpos49" "gpos50" "gpos51" [57] "gpos52" "gpos53" "gpos54" "gpos55" "gpos56" "gpos57" "gpos58" [64] "gpos59" "gpos60" "gpos61" "gpos62" "gpos63" "gpos64" "gpos65" [71] "gpos66" "gpos67" "gpos68" "gpos69" "gpos70" "gpos71" "gpos72" [78] "gpos73" "gpos74" "gpos75" "gpos76" "gpos77" "gpos78" "gpos79" [85] "gpos80" "gpos81" "gpos82" "gpos83" "gpos84" "gpos85" "gpos86" [92] "gpos87" "gpos88" "gpos89" "gpos90" "gpos91" "gpos92" "gpos93" [99] "gpos94" "gpos95" "gpos96" "gpos97" "gpos98" "gpos99" "gpos100" ## If you know the cytoband color you can map it like this (example below using fake sampled) dm3$gieStain <- paste0("gpos", sample(1:100,size = length(dm3), replace = TRUE)) ## or you just assign some color Please feel free to post your question in github issue page <https: github.com="" tengfei="" ggbio="" issues=""> cheers Tengfei On Wed, Aug 6, 2014 at 11:45 AM, Mark Dunning <mark.dunning at="" gmail.com=""> wrote: > Hi all, > > I'm trying to plot an ideogram for the "dm3" genome using ggbio. I believe > the following should work (it did for previous version of BioC). > > plotIdeogram(genome = "dm3") > > However, I get an error. > > Error in FUN("dm3"[[1L]], ...) : object 'cytobands' not found > > > In the code I can't see where cytobands is defined. How can I get the > ideogram for dm3. > > Regards, > > Mark > > Ideogram(obj, xlabel = xlabel, subchr = subchr, aspect.ratio = > aspect.ratio, > color = color, fill = fill, alpha = alpha, size = size, > zoom.region = zoom.region, > zoom.offset = zoom.offset, genome = genome) > debug: { > if (missing(obj)) { > data(ideoCyto, package = "biovizBase") > if (genome %in% names(ideoCyto)) { > obj <- ideoCyto[[genome]] > } > else { > obj <- getIdeogram(genome = genome, subchr = subchr, > cytobands = cytobands) > > > > > > sessionInfo()R version 3.1.0 (2014-04-10) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > LC_TIME=en_GB.UTF-8 > [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 > LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 > LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] rtracklayer_1.24.2 GenomicRanges_1.16.2 GenomeInfoDb_1.0.2 > IRanges_1.22.4 > [5] ggbio_1.12.8 ggplot2_1.0.0 BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.26.0 BatchJobs_1.2 BBmisc_1.6 > [4] Biobase_2.24.0 BiocParallel_0.6.0 biomaRt_2.20.0 > [7] Biostrings_2.32.1 biovizBase_1.12.1 bitops_1.0-6 > [10] brew_1.0-6 BSgenome_1.32.0 cluster_1.15.2 > [13] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > [16] dichromat_2.0-0 digest_0.6.4 fail_1.2 > [19] foreach_1.4.1 Formula_1.1-1 > GenomicAlignments_1.0.0 > [22] GenomicFeatures_1.16.0 grid_3.1.0 gridExtra_0.9.1 > [25] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.6 > [28] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-32 > [31] munsell_0.4.2 plyr_1.8.1 proto_0.3-10 > [34] RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1 > [37] reshape2_1.4 Rsamtools_1.16.0 RSQLite_0.11.4 > [40] scales_0.2.4 sendmailR_1.1-2 splines_3.1.0 > [43] stats4_3.1.0 stringr_0.6.2 survival_2.37-7 > [46] tools_3.1.0 VariantAnnotation_1.10.0 XML_3.98-1.1 > [49] XVector_0.4.0 zlibbioc_1.10.0 > > [[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 COMMENTlink written 5.3 years ago by Tengfei Yin490
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