RCircos (version 1.2.2)

RCircos.Scatter.Plot: Scater Plot for One Data Track

Description

Draw one track of scatter plot. RCircos core components and graphics device must be initialized before drawing.

Usage

RCircos.Scatter.Plot(scatter.data=NULL, data.col=4, 
    track.num=NULL, side=c("in", "out"), by.fold=0,
    min.value=NULL, max.value=NULL, inside.pos=NULL, 
    outside.pos=NULL, genomic.columns=3, is.sorted=TRUE)

Arguments

scatter.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.

by.fold

Zero or a positive float number, if it is greater than zero, any data point with a value greater than or equal to the by.fold will be plot as red color and data points with values less or equal to the negative by.fold will be plot as blue colr. Otherwise, black color is used.

min.value

Numeric, minimum value of scatter plot data.

max.value

Numeric, maximum value of scatter plot data

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.

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"), 
	tracks.inside=10, tracks.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", by.fold=1)
# }