vsDEGMatrix: Differential gene expression matrix

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

Description

This function allows you to visualize the number of differentially expressed genes (DEG) at a given #' adjusted P-value for each experimental treatment level. Higher color intensity correlates to a higher number of DEGs.

Usage

vsDEGMatrix(data, padj = 0.05, d.factor = NULL, type = c("cuffdiff",
  "deseq", "edger"), title = TRUE, legend = TRUE, grid = TRUE)

Arguments

data	output generated from calling the main routines of either 'cuffdiff', 'DESeq2', or 'edgeR' analyses. For 'cuffdiff', this will be a '*_exp.diff' file. For 'DESeq2', this will be a generated object of class 'DESeqDataSet'. For 'edgeR', this will be a generated object of class 'DGEList'.
padj	a user defined adjusted p-value cutoff point. Defaults to '0.05'.
d.factor	a specified factor; for use with 'DESeq2' objects only. This input equates to the first parameter for the contrast argument when invoking the 'results()' function in 'DESeq2'. Defaults to 'NULL'
type	an analysis classifier to tell the function how to process the data. Must be either 'cuffdiff', 'deseq', or 'edger'. 'cuffdiff' must be used with 'cuffdiff' data; 'deseq' must be used for 'DESeq2' output; 'edgeR' must be used with 'edgeR' data. See the 'data' parameter for further details.
title	display the main title of plot. Logical; defaults to 'TRUE'. If set to 'FALSE', no title will display in plot.
legend	display legend of plot. Logical; defaults to 'TRUE'. If set to 'FALSE', no legend will display in plot.
grid	display major and minor axis lines. Logical; defaults to 'TRUE'. If set to 'FALSE', no axis lines will display in plot.

Value

An object created by ggplot

Author(s)

Brandon Monier, [e-mail]

Examples

# cuffdiff example
data("df.cuff")
vsDEGMatrix(
 df.cuff, padj = 0.05, d.factor = NULL, type = 'cuffdiff', 
 title = TRUE, legend = TRUE, grid = TRUE
)

# DESeq2 example
data("df.deseq")
require(DESeq2)
vsDEGMatrix(
 df.deseq, padj = 0.05, d.factor = 'condition', type = 'deseq', 
 title = TRUE, legend = TRUE, grid = TRUE
)

# edgeR example
data("df.edger")
require(edgeR)
vsDEGMatrix(
 df.edger, padj = 0.05, d.factor = NULL, type = 'edger', 
 title = TRUE, legend = TRUE, grid = TRUE
)

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