TargetExperiment-plotGeneAttrPerFeat: Plot the attribute value for all the features of a selected...

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

plotGeneAttrPerFeat plots the achieved performance for each feature for a particular gene. The resulting graph shows one bar per each gene feature with heights according to its attribute value.

Usage

plotGeneAttrPerFeat(object, geneID, overlap=FALSE, level="feature")

## S4 method for signature 'TargetExperiment'
plotGeneAttrPerFeat(object, geneID, overlap=FALSE,
level="feature")

Arguments

object	TargetExperiment object.
geneID	Character indicating the ID of the selected gene.
overlap	Logical indicating if the amplicons should be collapsed in overlapped regions.
level	Character indicating the level of the plot. Can be 'feature', to plot the features' attribute; 'region', to plot overlapped regions' attribute or 'both'to generate the two previos plots

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

plotAttrExpl

Examples

## Loading the TargetExperiment object
data(ampliPanel, package="TarSeqQC")
## Exploring amplicon attribute values for a particular gene
# Ignoring amplicon overlapping 
g<-plotGeneAttrPerFeat(ampliPanel, geneID="gene4")
# Adjust text size
g<-g+theme(title=element_text(size=16), axis.title=element_text(size=16),
legend.text=element_text(size=14))
if(interactive()){
g
}
# Considering amplicon overlapping 
g<-plotGeneAttrPerFeat(ampliPanel, geneID="gene4", overlap=TRUE, level="both")
# Adjust text size
g<-g+theme(title=element_text(size=16), axis.title=element_text(size=16),
legend.text=element_text(size=14))
if(interactive()){
g
}

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