Draw Polygons on One Data Track

Plot polygons with different height and different locations inside of a track. Polygon plot is an alternative bar plot that takes both positive and negative height values and genomic intervals with different lengths. Plot data should have genomic positions(chromosome names, start and end positions) as well as height values. Optional column for polygon colors may follow.

Usage

RCircos.Polygon.Plot(polygon.data=NULL, data.col=NULL,  
    track.num=NULL, side=c("in", "out"), border.col=NULL,  
    polygon.col="pink", min.value=NULL, max.value=NULL,  
    inside.pos=NULL, outside.pos=NULL, genomic.columns=3,  
    is.sorted = TRUE)

Arguments

polygon.data

A data frame with three columns for genomic positions, one or columns for polygon heights, 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.

border.col

Vector of color names for border color, default null.

polygon.col

Color name for fill of polygon.

min.value

Numeric, minimum value in data column of polygon data.

max.value

Numeric, maximum value in data column of polygon 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.

Author

Henry Zhang

Examples

if (FALSE) { # \dontrun{
library(RCircos);
data(UCSC.HG19.Human.CytoBandIdeogram);
data(RCircos.Polygon.Data);

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

RCircos.Polygon.Plot(RCircos.Polygon.Data,  
    track.num=1, side="in")
} # }