Question: plotting both
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5.9 years ago by
Guest User12k
Guest User12k wrote:
I???ve been trying to plot one chromosome on one hemisphere of a circos plot, and then plot a zoomed in view of a particular region on the same chromosome on the other hemisphere of the plot. I???ve set up the plot so that there is a gap between the two hemispheres. However, in practice, the ideogram on the zoomed in region extend into other hemisphere, and gene names are drawn on the other hemisphere. How do I go about correcting this problem? -- output of sessionInfo(): > 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] splines grid parallel stats graphics grDevices utils [8] datasets methods base other attached packages: [1] chipseq_1.12.0 ShortRead_1.20.0 [3] Rsamtools_1.14.2 BiocInstaller_1.12.0 [5] OmicCircos_1.0.0 rtracklayer_1.22.3 [7] Biobase_2.22.0 BSgenome.Hsapiens.UCSC.hg18_1.3.19 [9] BSgenome_1.30.0 Biostrings_2.30.1 [11] faraway_1.0.5 plyr_1.8 [13] pscl_1.04.4 vcd_1.3-1 [15] gam_1.09 coda_0.16-1 [17] mvtnorm_0.9-9997 MASS_7.3-29 [19] Hmisc_3.14-0 Formula_1.1-1 [21] survival_2.37-7 lattice_0.20-24 [23] cluster_1.14.4 GenomicRanges_1.14.4 [25] XVector_0.2.0 IRanges_1.20.6 [27] BiocGenerics_0.8.0 Matrix_1.1-2 loaded via a namespace (and not attached): [1] bitops_1.0-6 colorspace_1.2-4 hwriter_1.3 [4] latticeExtra_0.6-26 RColorBrewer_1.0-5 RCurl_1.95-4.1 [7] stats4_3.0.2 tools_3.0.2 XML_3.95-0.2 [10] zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 5.9 years ago by Hu, Ying NIH/NCI [E]50 • written 5.9 years ago by Guest User12k
Answer: plotting both
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gravatar for Hu, Ying NIH/NCI [E]
5.9 years ago by
United States
Hu, Ying NIH/NCI [E]50 wrote:
please try: zoom <- c(1, 1, start, end, 180, 358); "start" and "end" are the positions in which you wanted to zoom. Ying ________________________________________ From: Mark Carty [guest] [guest@bioconductor.org] Sent: Monday, February 03, 2014 10:47 AM To: bioconductor at r-project.org; mac449 at cornell.edu Cc: Hu, Ying (NIH/NCI) [E] Subject: Re: plotting both I?ve been trying to plot one chromosome on one hemisphere of a circos plot, and then plot a zoomed in view of a particular region on the same chromosome on the other hemisphere of the plot. I?ve set up the plot so that there is a gap between the two hemispheres. However, in practice, the ideogram on the zoomed in region extend into other hemisphere, and gene names are drawn on the other hemisphere. How do I go about correcting this problem? -- output of sessionInfo(): > 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] splines grid parallel stats graphics grDevices utils [8] datasets methods base other attached packages: [1] chipseq_1.12.0 ShortRead_1.20.0 [3] Rsamtools_1.14.2 BiocInstaller_1.12.0 [5] OmicCircos_1.0.0 rtracklayer_1.22.3 [7] Biobase_2.22.0 BSgenome.Hsapiens.UCSC.hg18_1.3.19 [9] BSgenome_1.30.0 Biostrings_2.30.1 [11] faraway_1.0.5 plyr_1.8 [13] pscl_1.04.4 vcd_1.3-1 [15] gam_1.09 coda_0.16-1 [17] mvtnorm_0.9-9997 MASS_7.3-29 [19] Hmisc_3.14-0 Formula_1.1-1 [21] survival_2.37-7 lattice_0.20-24 [23] cluster_1.14.4 GenomicRanges_1.14.4 [25] XVector_0.2.0 IRanges_1.20.6 [27] BiocGenerics_0.8.0 Matrix_1.1-2 loaded via a namespace (and not attached): [1] bitops_1.0-6 colorspace_1.2-4 hwriter_1.3 [4] latticeExtra_0.6-26 RColorBrewer_1.0-5 RCurl_1.95-4.1 [7] stats4_3.0.2 tools_3.0.2 XML_3.95-0.2 [10] zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink written 5.9 years ago by Hu, Ying NIH/NCI [E]50
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