vsMAMatrix {vidger} | R Documentation |
This function allows you to generate MA plots for all possible treatment combinations for a given factor in either a cuffdiff, DESeq2, or edgeR data set.
vsMAMatrix(data, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"), padj = 0.05, y.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)
data |
output generated from calling the main routines of either
|
d.factor |
a specified factor; for use with |
type |
an analysis classifier to tell the function how to process the
data. Must be either |
padj |
a user defined adjusted p-value cutoff point.
Defaults to |
y.lim |
set manual limits (boundaries) to the y axis. Defaults to
|
lfc |
log fold change level for setting conditonals. If no user
input is added ( |
title |
display the main title of plot. Logical; defaults to
|
legend |
display legend of plot. Logical; defaults to |
grid |
display major and minor axis lines. Logical; defaults to
|
counts |
displays the number of differentially expressed genes for
each treatment comparison. Defaults to |
data.return |
returns data output of plot. Logical; defaults to
|
xaxis.text.size |
change the font size of the |
yaxis.text.size |
change the font size of the |
xaxis.title.size |
change the font size of the |
yaxis.title.size |
change the font size of the |
main.title.size |
change the font size of the plot title text.
Defaults to |
legend.text.size |
change the font size of the legend body text.
Defaults to |
facet.title.size |
change the font size of the facet wrap title text.
Defaults to |
An object created by ggplot
Brandon Monier, brandon.monier@sdstate.edu
# Cuffdiff example data("df.cuff") vsMAMatrix( data = df.cuff, d.factor = NULL, type = "cuffdiff", padj = 0.05, y.lim = NULL, lfc = 1, title = TRUE, grid = TRUE, counts = TRUE, data.return = FALSE ) # DESeq2 example data("df.deseq") require(DESeq2) vsMAMatrix( data = df.deseq, d.factor = "condition", type = "deseq", padj = 0.05, y.lim = NULL, lfc = 1, title = TRUE, grid = TRUE, counts = TRUE, data.return = FALSE ) # edgeR example data("df.edger") require(edgeR) vsMAMatrix( data = df.edger, d.factor = NULL, type = "edger", padj = 0.05, y.lim = NULL, lfc = 1, title = TRUE, grid = TRUE, counts = TRUE, data.return = FALSE ) # Extract data frame from visualization data("df.cuff") tmp <- vsMAMatrix( data = df.cuff, d.factor = NULL, type = "cuffdiff", padj = 0.05, y.lim = NULL, lfc = 1, title = TRUE, grid = TRUE, counts = TRUE, data.return = TRUE ) df_mamat <- tmp[[1]] ## or use tmp$data head(df_mamat) # Show plot from object (see prior example for more details) tmp[[2]] ## or use tmp$plot