vsVolcanoMatrix: Volcano plot matrix from log_{2} fold changes and...

In vidger: Create rapid visualizations of RNAseq data in R

Description

This function allows you to extract necessary results-based data from either a DESeq2 object, edgeR object, or cuffdiff data frame 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,
  xaxis.text.size = 9, yaxis.text.size = 9, xaxis.title.size = 10,
  yaxis.title.size = 10, main.title.size = 15, legend.text.size = 9,
  facet.title.size = 10)

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 FALSE.
xaxis.text.size	change the font size of the x-axis text. Defaults to 9.
yaxis.text.size	change the font size of the y-axis text. Defaults to 9.
xaxis.title.size	change the font size of the x-axis title text. Defaults to 10.
yaxis.title.size	change the font size of the y-axis title text. Defaults to 10.
main.title.size	change the font size of the plot title text. Defaults to 15.
legend.text.size	change the font size of the legend body text. Defaults to 9.
facet.title.size	change the font size of the facet wrap title text. Defaults to 10.

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)

# Show plot from object (see prior example for more details)
tmp[[2]] ## or use tmp$plot

vidger documentation built on Nov. 8, 2020, 5:27 p.m.