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

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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

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 [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

See Also

plot

Examples

## 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.