TarSeqQC (version 1.2.0)

plotFeature: Plot read profiles for a particular feature.

Description

plotFeature plots the achieved performance for each feature/gene. The resulting graph shows one bar per each feature/gene with heights 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

plotFeature(object, featureID, SNPs = TRUE, xlab = "", title = "", size = 0.5, BPPARAM = bpparam())
"plotFeature"(object, featureID, SNPs = TRUE, xlab = "", title = featureID, size = 0.5, BPPARAM = bpparam())

Arguments

object

TargetExperiment object.

featureID

Character indicating the ID of the feature.

SNPs

Logical flag indicating if SNPs should be plotted.

xlab

Character containing the axis x label.

title

Character containing the plot title.

size

Numeric indicating the size of line plots.

BPPARAM

An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

ggplot2 graphics.

See Also

plotRegion

Examples

if(interactive()){
## loading TargetExperiment object
data(ampliPanel, package="TarSeqQC")
## Defining bam file, bed file and fasta file names and paths
setBamFile(ampliPanel)<-system.file("extdata", "mybam.bam",
    package="TarSeqQC", mustWork=TRUE)
setFastaFile(ampliPanel)<-system.file("extdata", "myfasta.fa",
    package="TarSeqQC", mustWork=TRUE)

# Exploring the read count profile for a particular amplicon
g<-plotFeature(ampliPanel, featureID="AMPL20")
g
}