expressionBarplot {cummeRbund} | R Documentation

## Barplot

### 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

[Package cummeRbund version 2.28.0 Index]