TargetExperimentList-plotPoolPerformance: Plot pool performance of a TargetExperimentList object.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

plotPoolPerformance plots density and/or box-plot of the analyzed attribute achieved in each PCR pool. These graphics could be displayed together using the ggplot2 geom_violin method.

Usage

plotPoolPerformance(object, dens = FALSE, join = FALSE, log = TRUE,
    attributeThres = NULL)

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

Arguments

object	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. For it uses, dens should be TRUE.
log	Logical indicating if the attribute should be considered in log10 scale.
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.

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]

Examples

## Loading the TargetExperimentList object
data(TEList, package="TarSeqQC")
# Attribute boxplot and density plot exploration
g<-plotPoolPerformance(TEList,log=FALSE)
# x11(type="cairo")
if(interactive()){
g
}

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