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

In vidger: 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 log_{2} 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, highlight = NULL, data.return = FALSE,
  xaxis.text.size = 10, yaxis.text.size = 10, xaxis.title.size = 10,
  yaxis.title.size = 10, main.title.size = 15, legend.text.size = 9)

Arguments

x	treatment x for comparison (log_{2}(x/control)). This will be a factor level in your data.
y	treatment y for comparison (log_{2}(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.
highlight	character string of IDs that will be highlighted. Set to NULL if you do not want highlighted data.
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.
xaxis.text.size	change the font size of the x-axis text. Defaults to 10.
yaxis.text.size	change the font size of the y-axis text. Defaults to 10.
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.

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
)

# Highlight IDs
data("df.deseq")
require(DESeq2)
hl <- c(
    "FBgn0022201",
    "FBgn0003042",
    "FBgn0031957",
    "FBgn0033853",
    "FBgn0003371"
)
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, highlight = hl
)

# 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]] ## or use tmp$data
head(df_ma)

# 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.