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Last data update: 2014.03.03

R: Volcano Plot

csVolcano

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

The following object is masked from 'package:GenomicRanges':

    promoters

The following object is masked from 'package:IRanges':

    promoters

The following object is masked from 'package:BiocGenerics':

    conditions

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cummeRbund/csVolcano.Rd_%03d_medium.png", width=480, height=480)
> ### Name: csVolcano
> ### Title: Volcano Plot
> ### Aliases: csVolcano csVolcanoMatrix csVolcano,CuffData-method
> ###   csVolcanoMatrix,CuffData-method csVolcano,CuffFeatureSet-method
> 
> ### ** 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
Warning message:
Removed 40 rows containing missing values (geom_point). 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>