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

Description Usage Arguments Value Author(s) Examples

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

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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, brandon.monier@sdstate.edu

Examples

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# 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.