Point Plot for One Data Track

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

Henry Zhang

Examples

if (FALSE) { # \dontrun{
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)
} # }