csVolcano {cummeRbund} | R Documentation |
Creates a volcano plot of log fold change in expression vs -log(pval) for a pair of samples (x,y)
## 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(),...)
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 |
This creates a 'volcano' plot of fold change vs. significance for a pairwise comparison of genes or features across two different samples.
A ggplot2 plot object
None
Loyal A. Goff
None.
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