sim.circos {OmicCircos} | R Documentation

## circular data simulation

### Description

This function generates data for user to test the circos functions

### Usage

      sim.circos(seg=10, po=c(20,50), ind=10, link=10, link.pg=10);

### Arguments

`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.

### Value

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

### Author(s)

Ying Hu <yhu@mail.nih.gov> Chunhua Yan <yanch@mail.nih.gov>

### References

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

### Examples

    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()

[Package OmicCircos version 1.28.0 Index]