[BioC] plotting both

[Hu, Ying (NIH/NCI) [E]]

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 at 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


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