RCircos.Point.Plot: Point Plot for One Data Track

In RCircos: Circos 2D Track Plot

Point Plot for One Data Track

Description

Plot points on a track without track outlines and sub-track lines. The size and location od each point can be adjusted with the data values. RCircos core components and graphic device must be initialized first.

Usage

RCircos.Point.Plot(point.data=NULL, data.col=4, 
    track.num=NULL, side=c("in", "out"), 
    min.value=NULL, max.value=NULL, 
    point.type=19, with.height=TRUE, 
    with.size=FALSE, point.scale=1, 
    inside.pos=NULL, outside.pos=NULL, 
    genomic.columns=3,  is.sorted=TRUE)

Arguments

point.data	A data frame with leading columns of chromosome names, start position and/or end position of each data point followed by data values for one or more samples
data.col	Non-negative integer, representing the ordinal number of the column in input dataset that contains the data to be plotted.
track.num	Non-negative integer, representing the ordinal number of the plot track where the lines will be plotted.
side	Character vector, either "in" or "out", representing the position related to chromosome ideogram.
min.value	Numeric, minimum value of point data.
max.value	Numeric, maximum value of point data
point.type	Non-negative integer for pch. Default is 19.
with.height	Logic, if TURE, the location of each point will be adjusted according to the data value.
with.size	Logic, if TURE, the size of each point will be adjusted according to the data value.
point.scale	Non-negative numeric, more scale for point size, must be greater than or equal to 1.
inside.pos	Non-negative numeric, inside position (relative to the centre of plot area) of the track.
outside.pos	Non-negative numeric, outside position (relative to the centre of plot area) of the track.
genomic.columns	Non-negative integer, total number of columns for genomic position in each row. Must be either 3 or 2.
is.sorted	Logic, whether the data is sorted by chromosome names and start positions.

Author(s)

Henry Zhang

Examples

## Not run: 
library(RCircos)
data(UCSC.HG19.Human.CytoBandIdeogram)

RCircos.Set.Core.Components(
	cyto.info=UCSC.HG19.Human.CytoBandIdeogram,
	chr.exclude=c("chrX", "chrY"), 
	num.inside=10, num.outside=0)

RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()

data(RCircos.Scatter.Data)
RCircos.Scatter.Plot(RCircos.Scatter.Data, 
	data.col=5, track.num=4, side="in", 
	with.height=TRUE, with.size=FALSE)

## End(Not run)

RCircos documentation built on March 18, 2022, 7:59 p.m.