R: Point Plot for One Data Track

RCircos.Point.Plot {RCircos} | R Documentation

## 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)

[Package RCircos version 1.2.0 Index]