TargetExperimentList-plotGlobalAttrExpl: Plot attribute exploration of a TargetExperimentList object.

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

Description

plotGlobalAttrExpl displays box-plot of the analyzed achieved attribute values along all samples and at a feature level. This graphic could include density plot together the corresponding box-plot using the ggplot2 geom_violin method.

Usage

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plotGlobalAttrExpl(object, attributeThres = c(0, 1, 50, 200, 500, Inf),
    dens = FALSE, log = FALSE, pool = FALSE, featureLabs = FALSE,
    medianMarg = NULL)

## S4 method for signature 'TargetExperimentList'
plotGlobalAttrExpl(object,
    attributeThres = c(0, 1, 50, 200, 500, Inf), dens = FALSE, log = FALSE,
    pool = FALSE, featureLabs = FALSE, medianMarg = NULL)

Arguments

object

TargetExperimentList class object.

attributeThres

Numeric indicating the attribute interval extreme values.

dens

Logical indicating if boxplot and density function should be plotted together using the ggplot2 geom_violin method or only the boxplot (dens=FALSE) should be displayed.

log

Logical indicating if the attribute should be considered in log10 scale.

pool

Logical indicating if the plots should be performed for each pool separately

featureLabs

logical indicating if feature names should be plotted

medianMarg

numeric indicating the percentage of the median attribute value to be plotted as lines. If it is NULL no line will be displayed

Value

ggplot2 graphics.

Note

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

See Also

plot

Examples

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## Loading the TargetExperimentList object
data(TEList, package="TarSeqQC")

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

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.