Question

extdata missing for non-human OmicCircos plots?

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micahgearhart • 0

@micahgearhart-6825

Last seen 10.1 years ago

United States

Has anyone been able to use a non-human genome with OmicCircos? The documentation/paper claim hg18/hg19/mm9/mm10 are supported but it doesn't look like the proper extdata for mouse is included with the package.

I tried to munge the UCSC cytogentic data into the right format but it looks like there is a different way of reading the extdata than user supplied dataframes. The following code will reproduce the problem and show the plot differences.

library("OmicCircos")
par(mar=c(2, 2, 2, 2))
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="")
circos(R=200, type="chr", cir="hg18", print.chr.lab=TRUE, W=4)

#cir Error
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="")
circos(R=200, type="chr", cir="mm9", print.chr.lab=TRUE, W=4)

dir(paste0(.libPaths(),"/OmicCircos/data"))
data(UCSC.hg18.chr)
data(UCSC.hg18)

#recreate mm9 data
library("biovizBase")
mm9IdeogramCyto <- as.data.frame(getIdeogram("mm9", cytoband = TRUE))
UCSC.mm9.chr<-mm9IdeogramCyto[,c("seqnames","start","end","name","gieStain")]
colnames(UCSC.mm9.chr)<-c("chrom","chromStart","chromEnd","name","gieStain")
UCSC.mm9<-as.data.frame(segAnglePo(seg.dat=UCSC.mm9.chr,seg=paste0("chr",c(rep(1:19),"X","Y"))),stringsAsFactors=F)
#seq data
head(UCSC.hg18)
head(UCSC.mm9)

#cyto data
head(UCSC.hg18.chr)
head(UCSC.mm9.chr)

#
par(mar=c(2, 2, 2, 2))
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="")
circos(R=200, type="chr", cir="mm9", print.chr.lab=TRUE, W=4) #doesn't find it

plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="")
circos(R=200, type="chr", cir=UCSC.mm9, print.chr.lab=TRUE, W=4)

plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="")
circos(R=200, type="chr", cir=UCSC.hg18, print.chr.lab=TRUE, W=4) #reads df different than extdata

sessionInfo()

My sessionInfo(). I also tried it with R 3.1.1.

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C         LC_MONETARY=C
[6] LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C         LC_TELEPHONE=C
[11] LC_MEASUREMENT=C     LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] rtracklayer_1.25.16 biovizBase_1.13.11 OmicCircos_1.4.0 GenomicRanges_1.17.42 GenomeInfoDb_1.1.22
[6] IRanges_1.99.28 S4Vectors_0.2.4 BiocGenerics_0.11.5

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.27.16     BBmisc_1.7                BSgenome_1.33.9           BatchJobs_1.4
[5] Biobase_2.25.0            BiocParallel_0.99.22      Biostrings_2.33.14        DBI_0.3.1
[9] Formula_1.1-2             GenomicAlignments_1.1.30 GenomicFeatures_1.17.15   Hmisc_3.14-5
[13] RColorBrewer_1.0-5        RCurl_1.95-4.3            RSQLite_0.11.4            Rcpp_0.11.2
[17] Rsamtools_1.17.34         VariantAnnotation_1.11.35 XML_3.98-1.1              XVector_0.5.8
[21] acepack_1.3-3.3           base64enc_0.1-2           biomaRt_2.21.1            bitops_1.0-6
[25] brew_1.0-6                checkmate_1.4             cluster_1.15.2            codetools_0.2-8
[29] colorspace_1.2-4          dichromat_2.0-0           digest_0.6.4              fail_1.2
[33] foreach_1.4.2             foreign_0.8-61            futile.logger_1.3.7       futile.options_1.0.0
[37] grid_3.1.0                iterators_1.0.7           lambda.r_1.1.6            lattice_0.20-29
[41] latticeExtra_0.6-26       munsell_0.4.2             nnet_7.3-8                plyr_1.8.1
[45] rpart_4.1-8               scales_0.2.4              sendmailR_1.2-1           splines_3.1.0
[49] stringr_0.6.2             survival_2.37-7           tools_3.1.0               zlibbioc_1.11.1

>

OmicCircos • 1.8k views

ADD COMMENT • link updated 9.7 years ago by Hu, Ying NIH/NCI [E] ▴ 50 • written 10.1 years ago by micahgearhart • 0

score 0 · Answer 1 · 2015-03-13

OmicCircos was updated http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html

The output files are at https://www.dropbox.com/s/xgixwithokmedbq/BioC_ext.pdf?dl=0 and https://www.dropbox.com/s/inyrt19qvphjg2e/BioC_ext2.pdf?dl=0 by the following codes

Thanks

rm(list=ls());

library("OmicCircos")

#recreate mm9 data
library("biovizBase")
mm9IdeogramCyto <- as.data.frame(getIdeogram("mm9", cytoband = TRUE))
UCSC.mm9.chr <- mm9IdeogramCyto[,c("seqnames","start","end","name","gieStain")]
colnames(UCSC.mm9.chr) <- c("chrom","chromStart","chromEnd","name","gieStain")
UCSC.mm9 <- as.data.frame(segAnglePo(seg.dat=UCSC.mm9.chr,seg=paste0("chr",c(rep(1:19),"X","Y"))),stringsAsFactors=F)

pdf("BioC_ext.pdf", 8,8);
par(mar=c(2, 2, 2, 2))
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="")

dir(paste0(.libPaths(),"/OmicCircos/data"))
data(UCSC.hg18.chr)
data(UCSC.hg18)

#seq data
head(UCSC.hg18)
head(UCSC.mm9)

#cyto data
head(UCSC.hg18.chr)
head(UCSC.mm9.chr)

circos(R=400, type="chr", cir="hg18", print.chr.lab=TRUE, W=8)
circos(R=340, type="chr", cir="mm9", print.chr.lab=TRUE, W=8)
circos(R=280, type="chr2", cir=UCSC.hg18, mapping=UCSC.hg18.chr, print.chr.lab=TRUE, W=8)
circos(R=220, type="chr2", cir=UCSC.mm9, mapping=UCSC.mm9.chr, print.chr.lab=TRUE, W=8)

dev.off();

rm(list=ls());

library("OmicCircos");

dir(paste0(.libPaths(),"/OmicCircos/data"))
data(UCSC.hg19.chr)
data(UCSC.hg19)

pdf("BioC_ext2.pdf", 8,8);
par(mar=c(2, 2, 2, 2))
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="")

R <- 400;
circos(R=R, type="chr", cir="hg19", print.chr.lab=TRUE, W=8)
for (i in 1:4){
R <- R - 40;
mychr <- paste0("chr", sample(1:22, 2));
chr.i <- which(UCSC.hg19.chr[,1] %in% mychr);
seg.v <- UCSC.hg19.chr[-chr.i,];
seg.c <- segAnglePo(seg.v, seg=as.character(unique(seg.v[,1])));
circos(R=R, type="chr2", cir=seg.c, mapping=seg.v, print.chr.lab=TRUE, W=8)
}

dev.off();