expressionBarplot: Barplot

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Description

A barplot of FPKM values with confidence intervals for a given gene, set of genes, or features of a gene (e.g. isoforms, TSS, CDS, etc).

Usage

## S4 method for signature 'CuffFeatureSet'
expressionBarplot(object, logMode=TRUE, pseudocount=1.0, showErrorbars=TRUE, showStatus=TRUE, replicates=FALSE, ...)

Arguments

object	An object of class ('CuffFeatureSet','CuffGeneSet','CuffFeature','CuffGene')
logMode	A logical value whether or not to draw y-axis on log10 scale. Default = FALSE.
pseudocount	Numerical value added to each FPKM during log-transformation to avoid errors.
showErrorbars	A logical value whether or not to draw error bars. Default = TRUE
showStatus	A logical value whether or not to draw visual queues for quantification status of a given gene:condition. Default = TRUE
replicates	A logical value whether or not to plot individual replicates or aggregate condition values.
...	Additional arguments.

Details

None

Value

A ggplot2 plot object

Note

Need to implement logMode and features for this plotting method.

Author(s)

Loyal A. Goff

References

None

Examples

	data(sampleData)
	PINK1 # sample CuffFeature object
	expressionBarplot(PINK1) #Barplot of PINK1 FPKM values
	expressionBarplot(PINK1@isoforms) #Barplot of PINK1 FPKM values faceted by isoforms

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.