plotAttrExpl {TarSeqQC} | R Documentation

## Plot attribute exploration of a TargetExperiment/TargetExperimentList object.

### Description

`plotAttrExpl` plots density and/or box-plot of the analyzed attribute at a feature level. These graphics could be displayed together using the ggplot2 geom_violin method. If panel's pools are present, one facet for each pool will be showed.

### Usage

    plotAttrExpl(object, dens = FALSE, join = FALSE, log = TRUE,
        pool = FALSE, ...)

    ## S4 method for signature 'TargetExperiment'
    plotAttrExpl(object, level = "feature",
        join = TRUE, log = TRUE, color = "blue")

    ## S4 method for signature 'TargetExperimentList'
    plotAttrExpl(object, dens = FALSE,
        join = FALSE, log = TRUE, pool = FALSE, attributeThres = NULL)

### Arguments

`object` | TargetExperiment/TargetExperimentList class object.
`dens` | Logical indicating if density plot should be included
`join` | Logical indicating if boxplot and density function should be plotted together using the ggplot2 geom_violin method.
`log` | Logical indicating if the attribute should be considered in log10 scale.
`pool` | Logical indicating if plots should be displayed for each pool separately
`...` | necessary arguments
`level` | Character 'feature' or 'gene' indicating at which level should be analyzed the attribute.
`color` | A character indicating a valid name color.
`attributeThres` | Numeric indicating the attribute interval extreme values. It is not a mandatory parameter but if it is specified,then the plots will be colored according to the interval in which falls the attribute median values.

### Value

ggplot2 graphics.

### Note

see full example in `TargetExperiment-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

### See Also

`plot`, `plotFeatPerform`

### Examples

    ## Loading the TargetExperiment object
    data(ampliPanel, package="TarSeqQC")

    # Attribute boxplot and density plot exploration
    g<-plotAttrExpl(ampliPanel,level="feature",join=TRUE, log=FALSE, color="blue")
    # x11(type="cairo")
    if(interactive()){
    g
    }
    ## Loading the TargetExperimentList object
    data(TEList, package="TarSeqQC")

    # Attribute boxplot and density plot exploration
    g<-plotAttrExpl(TEList, log=FALSE, pool=FALSE)
    # x11(type="cairo")
    if(interactive()){
    g
    }

[Package TarSeqQC version 1.24.0 Index]