vsScatterMatrix: Scatter plot matrix of log10(FPKM or CPM) values

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

Description

This function will generate a matrix of scatterplots for all possible treatment combinations with additional distribution info.

Usage

vsScatterMatrix(data, d.factor = NULL, type = c("cuffdiff", "deseq",
  "edger"), comp = NULL, title = TRUE, grid = TRUE, man.title = NULL)

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'.
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.
comp	treatments you would like to compare in the form of a vector. If no parameter is specified, all possible treatment comparisons will be made. Defaults to 'NULL'.
title	display the main title of plot. Logical; defaults to 'TRUE'. If set to 'FALSE', no title 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.
man.title	a manually specified title at the authors discretion. Defaults to 'NULL'.

Value

An object created by ggplot

Author(s)

Brandon Monier, [e-mail]

Examples

# Cuffdiff example
data("df.cuff")
vsScatterMatrix(
 data = df.cuff, d.factor = NULL, type = 'cuffdiff', 
 comp = NULL, title = TRUE, grid = TRUE, 
 man.title = 'Example title'
)

# DESeq2 example
data("df.deseq")
require(DESeq2)
vsScatterMatrix(
 data = df.deseq, d.factor = 'condition', type = 'deseq',
 comp = NULL, title = TRUE, grid = FALSE, man.title = NULL
)

# edgeR example
data("df.edger")
require(edgeR)
vsScatterMatrix(
 data = df.edger, d.factor = NULL, type = 'edger', 
 comp = c('WM', 'MM'), title = TRUE, grid = TRUE, 
 man.title = NULL
)

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