cummeRbund (version 2.14.0)

csVolcano: Volcano Plot

Description

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

Usage

"csVolcano"(object, x, y, alpha=0.05, showSignificant=TRUE,features=FALSE, xlimits = c(-20, 20), ...)
"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

Value

A ggplot2 plot object

Details

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

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