[BioC] plotIdeogram for non-human or mouse genome
Tengfei Yin
tengfei.yin at sbgenomics.com
Wed Aug 27 00:20:10 CEST 2014
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]]
>
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--
Tengfei Yin, PhD
Product Manager
Seven Bridges Genomics
sbgenomics.com
One Broadway FL 7
Cambridge, MA 02142
(617) 866-0446
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