plot {TarSeqQC} | R Documentation

## 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 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

    ## 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

    ## 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
    }

[Package TarSeqQC version 1.12.0 Index]