circos {OmicCircos} | R Documentation |
This is the main function of OmicCircos to draw circular plots.
circos(mapping=mapping, xc=400, yc=400, R=400, W=W, cir="", type="n", col.v=3, B=FALSE, print.chr.lab=TRUE, col.bar=FALSE, col.bar.po = "topleft", cluster=FALSE, order=NULL, scale=FALSE, cutoff = "n", zoom="", cex=1, lwd=1, col=rainbow(10, alpha=0.8)[7], side="")
mapping |
data frame or matrix containing mapping information and values. Column 1: the segment or chromosome ID; column 2: the position; column 3: the position label (optional) or the value and additional columns are the values. such as gene expression and copy number. Missing values are allowed and will be ignored. |
xc |
integer, the circle center x coordinate |
yc |
integer, the circle center y coordinate |
R |
integer, the circle radius |
W |
integer, the circle width |
cir |
genome reference name (hg19, mm10 ...) or data frame from segAnglePo function or data frame from user's mapping data |
.
type |
the type is one of
|
col.v |
column number. The column value will be displayed. If type=heatmap, the number is as the first column. |
B |
logical: draw background? |
print.chr.lab |
logical: draw chromosomes or segment labels? |
col.bar |
logical: draw col.bar? It is for type=heatmap. |
col.bar.po |
draw col.bar position, e.g. topleft, bottomright. |
cluster |
logical: cluster and draw Dendrogram at left coner? It is for type=heatmap only. |
order |
vector: chromosome or segment order |
scale |
logical: draw scale? |
cutoff |
numeric: for multiple samples |
zoom |
vector containing six values: start chromosome, end chromosome, start position, end position, start angle and end angle |
lwd |
numeric: line width |
cex |
numeric: fond or point sizes |
col |
character or vector: color names |
side |
character (in or out): for type=label(2) only |
... |
... |
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 <- "OmicCircos4vignette1.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, cir=db, type="chr", col=colors, print.chr.lab=TRUE, W=4, scale=TRUE); circos(R=360, cir=db, W=40, mapping=seg.v, col.v=3, type="l", B=TRUE, col=colors[1], lwd=2, scale=TRUE); circos(R=320, cir=db, W=40, mapping=seg.v, col.v=3, type="ls", B=FALSE, col=colors[9], lwd=2, scale=TRUE); circos(R=280, cir=db, W=40, mapping=seg.v, col.v=3, type="lh", B=TRUE, col=colors[7], lwd=2, scale=TRUE); circos(R=240, cir=db, W=40, mapping=seg.v, col.v=19, type="ml", B=FALSE, col=colors, lwd=2, scale=TRUE); circos(R=200, cir=db, W=40, mapping=seg.v, col.v=19, type="ml2", B=TRUE, col=colors, lwd=2); circos(R=160, cir=db, W=40, mapping=seg.v, col.v=19, type="ml3", B=FALSE, cutoff=5, 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)); dev.off() ## Not run: demo(OmicCircos4vignette1) demo(OmicCircos4vignette2) demo(OmicCircos4vignette3) demo(OmicCircos4vignette4) demo(OmicCircos4vignette5) demo(OmicCircos4vignette6) demo(OmicCircos4vignette7) demo(OmicCircos4vignette8) demo(OmicCircos4vignette9) demo(OmicCircos4vignette10) ## End(Not run)