TargetExperiment-plotFeatPerform: Plot feature performance of a TargetExperiment object.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

plotFeatPerform plots the achieved performance for each feature/gene. The resulting graph shows one bar per each feature/gene with height according to its attribute value. If complete is set as TRUE, two bar plots (feature and gene level) will be stored in the resulting ggplot object.

Usage

plotFeatPerform(object, attributeThres = c(0, 1, 50, 200, 500, Inf),
    complete = TRUE, log = TRUE, featureLabs = FALSE, sepChr = FALSE,
    legend = TRUE)

## S4 method for signature 'TargetExperiment'
plotFeatPerform(object, attributeThres = c(0, 1,
    50, 200, 500, Inf), complete = TRUE, log = TRUE, featureLabs = FALSE,
    sepChr = FALSE, legend = TRUE)

Arguments

object	TargetExperiment class object.
attributeThres	Numeric indicating the intervals extreme values.
complete	Logical indicating if the gene and feature level exploration should be plotted.
log	Logical indicating if the attribute should be considered in log10 scale.
featureLabs	Logical indicating if feature labels should be plotted.
sepChr	Logical indicating if the plot should show chromosome divisions.
legend	Logical indicating if legend should be plotted.

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

Examples

## Loading the TargetExperiment object
data(ampliPanel, package="TarSeqQC")

# Definition of the interval extreme values
attributeThres<-c(0,1,50,200,500, Inf)

# Plot panel overview in a feature performance plot
g<-plotFeatPerform(ampliPanel, attributeThres=attributeThres, log=FALSE, 
featureLabs=TRUE, sepChr=TRUE, legend=TRUE)
if(interactive()){
g
}

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