RCircos.Area.Plot: Paint Areas on One Data Track

In RCircos: Circos 2D Track Plot

Paint Areas on One Data Track

Description

Paint area on one data track with different height and different locations inside of a track. Plot types includes "mountain", "curtain", and "band". Plot data should have genomic positions(chromosome names, start and end positions) as well as height values. For band type plot, two columns of height values are required.

Usage

RCircos.Area.Plot(area.data=NULL, data.col=c(4,5),
    track.num=NULL, side=c("in", "out"), 
    plot.type=c("mountain", "curtain", "band"), 
    min.value=NULL, max.value=NULL, area.color="gray",
    border.col="black", inside.pos=NULL, outside.pos=NULL, 
    genomic.columns=3, is.sorted=TRUE)

Arguments

area.data	A data frame with two or three columns for genomic positions, one or more columns for heights of each data point, and an optional column for polygon colour.
data.col	Non-negative integer, representing the ordinal number of the column in input data set 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.
plot.type	Character vector, either "mountain", "curtain", or "band"
min.value	Numeric, minimum value in data column of polygon data.
max.value	Numeric, maximum value in data column of polygon data.
area.color	Color names for fill of the area.
border.col	Color name for border color, default null.
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);
data(RCircos.Polygon.Data);

RCircos.Set.Core.Components(  
    cyto.info=UCSC.HG19.Human.CytoBandIdeogram,  
    chr.exclude=NULL, tracks.inside=10, tracks.outside=5)  
RCircos.Set.Plot.Area();
RCircos.Chromosome.Ideogram.Plot()

load("RCircos/data/RCircos.Histogram.Data.RData")

area.data <- RCircos.Histogram.Data;
adj.value <- runif(nrow(area.data), 0, 0.4)
area.data["DataT"] <- 0.5 + adj.value
area.data["DataB"] <- 0.5 - adj.value

RCircos.Area.Plot(area.data, data.col=4, plot.type="mountain", 
    inside.pos=1.2, outside.pos=1.5, is.sorted=FALSE)

RCircos.Area.Plot(area.data, data.col=4, plot.type="curtain", 
    inside.pos=0.9, outside.pos=1.1, is.sorted=FALSE)

RCircos.Area.Plot(area.data, data.col=c(5,6), plot.type="band", 
    inside.pos=0.4, outside.pos=0.7, is.sorted=FALSE)
## End(Not run)

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