plot: Plot TargetExperiment object overview.

Description

plot allows a fast and simple representation of one feature panel using a polar histogram plot. Histogram bar reflects the percentage of features that have shown the analyzed attribute in a user setted interval. The resulting graph can be busy and might be better off saved.

Usage

"plot"(x, y, attributeThres = c(0, 1, 50, 200, 500, Inf), binSize = 1, spaceGene = 0.2, spaceChr = 1.2, innerRadius = 0.3, outerRadius = 1, guides = c(20, 40, 60, 80), alphaStart = -0.3, circleProportion = 0.95, direction = "inwards", chrLabels = FALSE)

Arguments

TargetExperiment class object.

not used but necessary for redefining the generic function.

attributeThres

Numeric indicating the interval extreme values.

binSize

Numeric indicating bin width. Should probably be left as 1, as other parameters are relative to it.

spaceGene

Numeric. Space between bins.

spaceChr

Numeric. Space between chromosomes.

innerRadius

Numeric. Radius of inner circle.

outerRadius

Numeric. Radius of outer circle.

guides

A vector with percentages to use for the white guide lines.

alphaStart

Numeric offset from 12 o'clock in radians.

circleProportion

Numeric proportion of the circle to cover.

direction

Character indicating if the increasing count goes from or to the centre.

chrLabels

Logical. Chromosome names must be plotted?.

Value

a ggplot2 graph.

References

http://www.r-bloggers.com/polar-histogram-pretty-and-useful/

Examples

Run this code

if(interactive()){
## Loading the TargetExperiment object
data(ampliPanel, package="TarSeqQC")
# Definition of the interval extreme values
attributeThres<-c(0,1,50,200,500, Inf)

## Plot panel overview
g<-plot(ampliPanel, attributeThres, chrLabels =TRUE)
g
}