OmicCircos (version 1.10.0)

circos: draw circular

Description

This is the main function of OmicCircos to draw circular plots.

Usage

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="")

Arguments

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

• "arc": arcs with variable radii
• "arc2": arcs with the fixed radius
• "b": bar charts
• "b2": bar charts (opposite side of cutoff value)
• "b3": bar charts with the same height
• "box": box plots
• "chr": plots of chromosomes or segments
• "chr2": plots of chromosomes or segments of partial genome
• "ci95": 95% confidence interval lines
• "h": histograms
• "heatmap": heatmaps
• "heatmap2": heatmaps with genomic coordinates
• "hightlight.link": link lines for zoom
• "hist": polygons for multiple samples
• "hl": highlight
• "l": lines
• "label": gene labels or text annotations
• "label2": gene labels or text annotations with the same circumference coordinate
• "lh": horizontal lines
• "link.pg": link polygons based on Bezier curve
• "link": link lines based on Bezier curve
• "link2": link lines with smaller intra-chromosome arcs
• "ls": lines in stair steps
• "ml": multiple lines (for more than 1 samples)
• "ml2": multiple horizontal lines
• "ml3": multiple lines in stair steps
• "ms": multiple points
• "quant75": 75% quantile lines
• "quant90": 90% quantile lines
• "s": dots
• "s2": dots with the fixed radius
• "s.sd": dots proportional to standard deviation
• "ss": dot sizes proportional to the values
• "sv": dot sizes proportional to the variances

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

...

...

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  <- "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)