vsVolcanoMatrix: Volcano plot matrix from log2 fold changes and...

In btmonier/vidger-nd: Create rapid visualizations of RNAseq data in R

Description

This function allows you to extract necessary results-based data from a DESEq object class to create a volcano plot (i.e. a scatter plot) of the negative log of the p-value versus the log of the fold change while implementing ggplot2 aesthetics for all possible combinations of treatments.

Usage

vsVolcanoMatrix(data, d.factor = NULL, type = c("cuffdiff", "deseq",
  "edger"), padj = 0.05, x.lim = NULL, lfc = NULL, title = TRUE,
  legend = TRUE, grid = TRUE, counts = TRUE, data.return = FALSE)

Arguments

data	a cuffdiff, DESeq2, or edgeR object.
d.factor	a specified factor; for use with DESeq2 objects only. Defaults to 'NULL'
type	an analysis classifier to tell the function how to process the data. Must be either 'cuffdiff', 'deseq', or 'edgeR'.
padj	a user defined adjusted p-value cutoff point. Defaults to '0.05'.
x.lim	set manual limits to the x axis. Defaults to 'NULL'.
lfc	log fold change level for setting conditonals. If no user input is added ('NULL'), value defaults to '1'.
title	show title of plot. Defaults to 'TRUE'.
legend	shows legend of plot. Defaults to 'TRUE'.
grid	show major and minor axis lines. Defaults to 'TRUE'.
counts	displays the number of differentially expressed genes for each treatment comparison. Defaults to 'TRUE'.
data.return	returns data output of plot if set to 'TRUE'. Defaults to 'FASLSE'.

Value

An object created by ggplot

Author(s)

Brandon Monier, [e-mail]

Examples

# Cuffdiff example
data("df.cuff")
vsVolcanoMatrix(
 data = df.cuff, d.factor = NULL, type = 'cuffdiff', 
 padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE, 
 grid = TRUE, counts = TRUE, data.return = FALSE
)

# DESeq2 example
data("df.deseq")
require(DESeq2)
vsVolcanoMatrix(
 data = df.deseq, d.factor = 'condition', type = 'deseq', 
 padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE, 
 grid = TRUE, counts = TRUE, data.return = FALSE
)

# edgeR example
data("df.edger")
require(edgeR)
vsVolcanoMatrix(
 data = df.edger, d.factor = NULL, type = 'edger', 
 padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE, 
 grid = TRUE, counts = TRUE, data.return = FALSE
)
                
# Extract data frame from visualization
data("df.cuff")
tmp <- vsVolcanoMatrix(
 data = df.cuff, d.factor = NULL, 
 type = 'cuffdiff', padj = 0.05, x.lim = NULL,
 lfc = 2, title = TRUE, grid = TRUE, 
 counts = TRUE, data.return = TRUE
)
df.vmat <- tmp[[1]]
head(df.vmat)

btmonier/vidger-nd documentation built on May 14, 2019, 12:44 p.m.