TargetExperiment-plotAttrExpl: Plot attribute exploration of a...

In TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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

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
}

TarSeqQC documentation built on Nov. 8, 2020, 6:03 p.m.