TargetExperiment-plotMetaDataExpl: Graphical exploration of a specific metadata column.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

plotMetaDataExpl plots density and box-plot of a specific metadata column. If the characteristic is nonnumerical, then a frequency plot is built.

Usage

plotMetaDataExpl(object, name = c("length", "gc", "pool"), log = FALSE,
    join = TRUE, absolute = FALSE, color = "blue")

## S4 method for signature 'TargetExperiment'
plotMetaDataExpl(object, name = c("length", "gc",
    "pool"), log = FALSE, join = TRUE, absolute = FALSE, color = "blue")

Arguments

object	TargetExperiment class object.
name	a character indicating the metadata column name that should be analyzed.
log	Logical indicating if the numerical metadata column should be considered in log10 scale.
join	Logical only for numerical variables. It indicates if boxplot and density function should be plotted together using the ggplot2 geom_violin method.
absolute	Logical indicating if the frequencies of the selected categorical metadata column should be in absolute scale. If absolute is FALSE the frequencies are in relative percentages.
color	A character indicating a valid name color.

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<-plotMetaDataExpl(ampliPanel, name="length")
if(interactive())
{
# x11(type="cairo")
g
}
# Explore amount of amplicons per gene
g<-plotMetaDataExpl(ampliPanel, name="gene", absolute=TRUE)
if(interactive())
{
# x11(type="cairo")
g
}

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