vsMAPlot: MA plot from mean expression and log fold changes from...

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

Description

This function allows you to extract necessary results-based data from different output files to create a MA plot (i.e. a scatter plot) of log2 fold changes versus normalized mean counts while implementing ggplot2 aesthetics.

Usage

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

Arguments

x	treatment 'x' for comparison (log2(x/control)). This will be a factor level in your data.
y	treatment 'y' for comparison (log2(y/control)). This will be a factor level in your data.
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'.
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.
padj	a user defined adjusted p-value cutoff point. Defaults to '0.05'.
y.lim	set manual limits (boundaries) to the y axis. Defaults to 'NULL'.
lfc	log fold change level for setting conditonals. If no user input is added ('NULL'), value defaults to '1'.
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.
data.return	returns data output of plot Logical; defaults to 'FALSE'. If set to 'TRUE', a data frame will also be called. Assign to object for reproduction and saving of data frame. See final example for further details.

Value

An object created by ggplot

Author(s)

Brandon Monier, [e-mail]

Examples

# Cuffdiff example
data("df.cuff")
vsMAPlot(
 x = 'hESC', y = 'iPS', data = df.cuff, d.factor = NULL, 
 type = 'cuffdiff', padj = 0.05, y.lim = NULL, lfc = 1, 
 title = TRUE, legend = TRUE, grid = TRUE, data.return = FALSE
)

# DESeq2 example
data("df.deseq")
require(DESeq2)
vsMAPlot(
 x = 'treated_paired.end', y = 'untreated_paired.end', 
 data = df.deseq, d.factor = 'condition', type = 'deseq', 
 padj = 0.05, y.lim = NULL, lfc = NULL, title = TRUE, 
 legend = TRUE, grid = TRUE, data.return = FALSE
)

# edgeR example
data("df.edger")
require(edgeR)
vsMAPlot(
 x = 'WM', y = 'MM', data = df.edger, d.factor = NULL, 
 type = 'edger', padj = 0.1, y.lim = NULL, lfc = 1, 
 title = FALSE, legend = TRUE, grid = TRUE, data.return = FALSE
)
                
# Extract data frame from visualization
data("df.cuff")
tmp <- vsMAPlot(
 x = 'hESC', y = 'iPS', data = df.cuff, 
 d.factor = NULL, type = 'cuffdiff', padj = 0.05, 
 y.lim = NULL, lfc = 1, title = TRUE, grid = TRUE, 
 data.return = TRUE
)
df.ma <- tmp[[1]]
head(df.ma)

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