vsDEGMatrix {vidger} | R Documentation |
This function allows you to visualize the number of differentially expressed genes (DEG) at a given adjusted P-value for each experimental treatment level. Higher color intensity correlates to a higher number of DEGs.
vsDEGMatrix(data, padj = 0.05, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"), title = TRUE, legend = TRUE, grid = TRUE, data.return = FALSE, grey.scale = FALSE, xaxis.text.size = 10, yaxis.text.size = 10, main.title.size = 15, legend.text.size = 10, legend.title.size = 12)
data |
output generated from calling the main routines of either
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padj |
a user defined adjusted p-value cutoff point. Defaults to
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d.factor |
a specified factor; for use with |
type |
an analysis classifier to tell the function how to process the
data. Must be either |
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
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data.return |
returns data output of plot. Logical; defaults to
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grey.scale |
displays grey color scheme instead of blue if set to
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xaxis.text.size |
change the font size of the |
yaxis.text.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 |
legend.title.size |
change the font size of the legend title text.
Defaults to |
An object created by ggplot
Brandon Monier, brandon.monier@sdstate.edu
# cuffdiff example data("df.cuff") vsDEGMatrix( df.cuff, padj = 0.05, d.factor = NULL, type = "cuffdiff", title = TRUE, legend = TRUE, grid = TRUE ) # DESeq2 example data("df.deseq") require(DESeq2) vsDEGMatrix( df.deseq, padj = 0.05, d.factor = "condition", type = "deseq", title = TRUE, legend = TRUE, grid = TRUE ) # edgeR example data("df.edger") require(edgeR) vsDEGMatrix( df.edger, padj = 0.05, d.factor = NULL, type = "edger", title = TRUE, legend = TRUE, grid = TRUE ) # Extract data frame from visualization data("df.edger") require(edgeR) tmp <- vsDEGMatrix( df.edger, padj = 0.05, d.factor = NULL, type = "edger", title = TRUE, legend = TRUE, grid = TRUE ) df_deg <- tmp[[1]] ## or use tmp$data head(df_deg) # Show plot from object (see prior example for more details) tmp[[2]] ## or use tmp$plot