csVolcano {cummeRbund} | R Documentation

## Volcano Plot

### Description

Creates a volcano plot of log fold change in expression vs -log(pval) for a pair of samples (x,y)

### Usage

    ## S4 method for signature 'CuffData'
    csVolcano(object, x, y, alpha=0.05, showSignificant=TRUE,features=FALSE, xlimits = c(-20, 20), ...)
    ## S4 method for signature 'CuffData'
    csVolcanoMatrix(object,alpha=0.05,xlimits=c(-20,20),mapping=aes(),...)

### Arguments

`object` | An object of class CuffData, CuffFeatureSet, or CuffGeneSet
`x` | Sample name from 'samples' table for comparison
`y` | Sample name from 'samples' table for comparison
`alpha` | Provide an alpha cutoff for visualizing significant genes
`showSignificant` | A logical value whether or not to distinguish between significant features or not (by color).
`features` | Will include all fields from 'features' slot in returned ggplot object. Useful for further manipulations of plot object using feature-level attributes (e.g. gene_type, class_code, etc)
`xlimits` | Set boundaries for x limits to avoid infinity plotting errors. [Default c(-20,20)]
`mapping` | Passthrough argument for ggplot aesthetics. Can be ignored completely.
`...` | Additional arguments

### Details

This creates a 'volcano' plot of fold change vs. significance for a pairwise comparison of genes or features across two different samples.

### Value

A ggplot2 plot object

### Note

None

### Author(s)

Loyal A. Goff

### References

None.

### Examples

    a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object
    genes<-a@genes #Create cuffData object for all genes
    v<-csVolcano(genes,"hESC","Fibroblasts") # Volcano plot of all genes for conditions x='hESC' and y='Fibroblast'
    v #print plot

[Package cummeRbund version 2.28.0 Index]