csVolcano: Volcano Plot

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

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

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