vsVolcanoMatrix {vidger} | R Documentation |
This function allows you to extract necessary results-based data from a DESEq object class 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.
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)
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 'FASLSE'. |
An object created by ggplot
Brandon Monier, brandon.monier@sdstate.edu
# 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)