Plot TargetExperiment object overview.

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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 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.

Usage

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## 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,...)

Arguments

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.

Value

a ggplot2 graph.

Note

see full example in TargetExperiment-class

see full example in TargetExperimentList-class

Author(s)

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

References

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

See Also

plotFeatPerform

Examples

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## 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
}

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