TargetExperiment-plot: Plot TargetExperiment object overview.
In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description Usage Arguments Value Note Author(s) References See Also Examples

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 set interval. The resulting graph can be busy and might be better off saved.

For TargetExperimentList objects, plot allows a fast and simple representation of several feature panels using a heatmap plot. Along the x-axis, the features are represented and patients/samples along the y-axis. Finally, each cell is colored according to the attribute interval.

## S3 method for class 'TargetExperiment'
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, ...)

## S3 method for class 'TargetExperimentList'
plot(x, y, attributeThres = c(0, 1, 50,
    200, 500, Inf), pool = FALSE, sampleLabs = TRUE, featureLabs = FALSE,...)

`x`	TargetExperiment/TargetExperimentList class object.
`y`	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 the inner circle.
`outerRadius`	Numeric. Radius of the 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 center.
`chrLabels`	Logical. Chromosome names must be plotted?.
`pool`	Logical indicating if the plots should be performed for each pool separately
`sampleLabs`	Logical. Sample names must be plotted?.
`featureLabs`	Logical. Feature names must be plotted?.
`...`	not used but necessary for redefining the generic function.

a ggplot2 graph.

see full example in TargetExperiment-class

see full example in TargetExperimentList-class

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

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

plotFeatPerform

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

## Plot panel overview
g<-plot(TEList, attributeThres=attributeThres, featureLabs =TRUE)
if(interactive()){
g
}