rc.plot.link {NetWeaver}

Plot Link

Description

Add a track of links on circos plot.

Usage

rc.plot.link(Data, track.id, data.col=NULL, color.col = NULL,
 max.lwd=1, sort.links=TRUE, arrow.length=0, arrow.angle=30, ...)

Arguments

Data

data.frame of at least four columns. See Details.

track.id

integer, the track number for plotting.

data.col

integer or character string, specifies the column of data.

color.col

integer or character string, specifies the column of colors.

max.lwd

integer, maximum line width.

sort.links

logical, whether to re-assign link start and end positions by sorting them. See details

arrow.length

length of the edges of the arrow head (in inches). See arrows

arrow.angle

angle from the shaft of the arrow to the edge of the arrow head. See arrows

...

further graphical parameters (from par), such as lty and lwd.

Details

Data must have at least four columns: Chr1, Pos1, Chr2 and Pos2, specifying the chromosomes and positions for the start and end points of the links. Additional columns may be used to specify the data, color and max line width.

If data.col is not NULL, the line width will be proportional to the values in column data.col with the maximum line width determined by max.lwd.

If sort.links is true, the links originate from the same chromosome will be sorted and equally spaced to minimize crossing.

Author(s)

Minghui Wang <[e-mail]>

See Also

rc.plot.histogram, rc.plot.ribbon

Examples

#This is not to be run alone. Please see tutorial vignette("netweaver") for usage.