RCircos.Heatmap.Plot {RCircos}

Draw Heatmap for One Data Track

Description

Draw one track of heatmap. RCircos core components and graphic device must be initialized before drawing.

Usage

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

Arguments

heatmap.data

A data frame with the first three columns as chromosome names, start position and 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 data set that contains the data to be plotted.

track.num

Non-negative Integer, representing the ordinal number of the plot track where the heatmap will be plotted.

side

Character vector, either "in" or "out", representing the position related to chromosome ideogram.

min.value

Numeric, minimum value for heatmap scale.

max.value

Numeric, maximum value for heatmap scale

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.Heatmap.Data)

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()

RCircos.Heatmap.Plot(RCircos.Heatmap.Data, data.col=5, 
	track.num=4, side="in")
RCircos.Heatmap.Plot(RCircos.Heatmap.Data, data.col=5, 
	side="in", inside.pos=0.9, outside.pos=1.2)

## End(Not run)