sim.circos {OmicCircos} | R Documentation |
This function generates data for user to test the circos functions
sim.circos(seg=10, po=c(20,50), ind=10, link=10, link.pg=10);
seg |
integer, the segment number. The default is 10. |
po |
vector, the segment positions. The default is c(20:50) |
ind |
integer, the number of samples. The default is 10. |
link |
integer, the number of links. The default is 10. |
link.pg |
integer, the number of link ploygons. The default is 10. |
sim.circos returns a list containing at least the following components:
seg.frame |
data.frame, segment data |
seg.mapping |
data.frame, mapping data |
seg.link |
data.fame, link data |
seg.link.pg |
data.frame, link polygon data |
Ying Hu <yhu@mail.nih.gov> Chunhua Yan <yanch@mail.nih.gov>
OmicCircos: an R package for simple and circular visualization of omics data. Cancer Inform. 2014 Jan 16;13:13-20. doi: 10.4137/CIN.S13495. eCollection 2014. PMID: 24526832 [PubMed] PMCID: PMC3921174
library(OmicCircos); options(stringsAsFactors = FALSE); set.seed(1234); ## initial values for simulation data seg.num <- 10; ind.num <- 20; seg.po <- c(20:50); link.num <- 10; link.pg.num <- 4; ## output simulation data sim.out <- sim.circos(seg=seg.num, po=seg.po, ind=ind.num, link=link.num, link.pg=link.pg.num); seg.f <- sim.out$seg.frame; seg.v <- sim.out$seg.mapping; link.v <- sim.out$seg.link link.pg.v <- sim.out$seg.link.pg seg.num <- length(unique(seg.f[,1])); ## select segments seg.name <- paste("chr", 1:seg.num, sep=""); db <- segAnglePo(seg.f, seg=seg.name); colors <- rainbow(seg.num, alpha=0.5); pdffile <- "OmicCircos4vignette3.pdf"; pdf(pdffile, 8, 8); par(mar=c(2, 2, 2, 2)); plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="", main=""); circos(R=400, type="chr", cir=db, col=colors, print.chr.lab=TRUE, W=4, scale=TRUE); circos(R=360, cir=db, W=40, mapping=seg.v, col.v=8, type="quant90", B=FALSE, col=colors, lwd=2, scale=TRUE); circos(R=320, cir=db, W=40, mapping=seg.v, col.v=3, type="sv", B=TRUE, col=colors[7], scale=TRUE); circos(R=280, cir=db, W=40, mapping=seg.v, col.v=3, type="ss", B=FALSE, col=colors[3], scale=TRUE); circos(R=240, cir=db, W=40, mapping=seg.v, col.v=8, type="heatmap", lwd=3); circos(R=200, cir=db, W=40, mapping=seg.v, col.v=3, type="s.sd", B=FALSE, col=colors[4]); circos(R=160, cir=db, W=40, mapping=seg.v, col.v=3, type="ci95", B=TRUE, col=colors[4], lwd=2); circos(R=150, cir=db, W=40, mapping=link.v, type="link", lwd=2, col=colors[c(1,7)]); circos(R=150, cir=db, W=40, mapping=link.pg.v, type="link.pg", lwd=2, col=sample(colors,link.pg.num)); the.col1=rainbow(10, alpha=0.5)[3]; highlight <- c(160, 410, 6, 2, 6, 10, the.col1, the.col1); circos(R=110, cir=db, W=40, mapping=highlight, type="hl", lwd=1); the.col1=rainbow(10, alpha=0.1)[3]; the.col2=rainbow(10, alpha=0.5)[1]; highlight <- c(160, 410, 3, 12, 3, 20, the.col1, the.col2); circos(R=110, cir=db, W=40, mapping=highlight, type="hl", lwd=2); dev.off()