segAnglePo {OmicCircos} | R Documentation |
This function creates a data frame and converts the segment pointer positions (linear coordinates) into angle values (the angle based coordinates along circumference). In the data frame, column 1 is unique segment or chromosome names; column 2 is the start angle; column 3 is the end angle; column 4 is the accumulative start position; column 5 is the accumulative end position; column 6 is the start position and column 7 is the end position for each segment or chromosome.
segAnglePo(seg.dat=seg.dat, seg=seg, angle.start=angle.start, angle.end=angle.end);
seg.dat |
the segment data should be a matrix or a data frame: column 1 is the segment name or chromosome name; column 2 is the segment start; column 3 is the segment end; column 4 is segment name2 (optional); and column 5 is segment description (optional). |
seg |
vector: segment names (optional) |
angle.start |
numeric: plot start angle, angle.start=0 by default (optional) |
angle.end |
numeric: plot end angle, angle.end=360 by default (optional) |
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 <- "OmicCircos4vignette2.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="box", B=TRUE, col=colors[1], lwd=0.1, scale=TRUE); circos(R=320, cir=db, W=40, mapping=seg.v, col.v=8, type="hist", B=TRUE, col=colors[3], lwd=0.1, scale=TRUE); circos(R=280, cir=db, W=40, mapping=seg.v, col.v=8, type="ms", B=TRUE, col=colors[7], lwd=0.1, scale=TRUE); circos(R=240, cir=db, W=40, mapping=seg.v, col.v=3, type="h", B=FALSE, col=colors[2], lwd=0.1); circos(R=200, cir=db, W=40, mapping=seg.v, col.v=3, type="s", B=TRUE, col=colors, lwd=0.1); circos(R=160, cir=db, W=40, mapping=seg.v, col.v=3, type="b", B=FALSE, col=colors, lwd=0.1); 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)); dev.off()