expressionPlot {cummeRbund} | R Documentation

## Expression Plot

### Description

A line plot (optionally with confidence intervals) detailing FPKM expression levels across conditions for a given gene(s) or feature(s)

### Usage

    ## S4 method for signature 'CuffFeature'
    expressionPlot(object, logMode=FALSE, pseudocount=1.0, drawSummary=FALSE, sumFun=mean_cl_boot, showErrorbars=TRUE, showStatus=TRUE, replicates=FALSE, facet = TRUE,...)

### Arguments

`object` | An object of class ('CuffFeature' or 'CuffGene')
`logMode` | A logical value to draw y-axis (FPKM) on log-10 scale. Default = FALSE.
`pseudocount` | A numeric value added to FPKM to avoid errors on log-10 transformation.
`drawSummary` | A logical valuie. Draws a 'summary' line with mean FPKM values for each condition.
`sumFun` | Function used to determine values for summary line. Default = mean_cl_boot
`showErrorbars` | A logical value whether or not to draw error bars.
`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.
`facet` | A logical value whether or not to facet the plot by feature id (default=TRUE).
`...` | Additional arguments

### Details

None

### Value

A ggplot2 plot object

### Note

None

### Author(s)

Loyal A. Goff

### References

None

### Examples

    	data(sampleData)
    	PINK1 # sample CuffFeature object
    	expressionPlot(PINK1) #Line plot of PINK1 FPKM values
    	expressionPlot(PINK1@isoforms) #Line plot of PINK1 FPKM values faceted by isoforms

[Package cummeRbund version 2.28.0 Index]