Description Usage Arguments Details Value Author(s) Examples
Create volcano plot from log2FC and adjusted pvalues data frame
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | degVolcano(
stats,
side = "both",
title = "Volcano Plot with Marginal Distributions",
pval.cutoff = 0.05,
lfc.cutoff = 1,
shade.colour = "orange",
shade.alpha = 0.25,
point.colour = "gray",
point.alpha = 0.75,
point.outline.colour = "darkgray",
line.colour = "gray",
plot_text = NULL
)
|
stats |
data.frame with two columns: logFC and Adjusted.Pvalue |
side |
plot UP, DOWN or BOTH de-regulated points |
title |
title for the figure |
pval.cutoff |
cutoff for the adjusted pvalue. Default 0.05 |
lfc.cutoff |
cutoff for the log2FC. Default 1 |
shade.colour |
background color. Default orange. |
shade.alpha |
transparency value. Default 0.25 |
point.colour |
colours for points. Default gray |
point.alpha |
transparency for points. Default 0.75 |
point.outline.colour |
Default darkgray |
line.colour |
Defaul gray |
plot_text |
data.frame with three columns: logFC, Pvalue, Gene name |
This function was mainly developed by @jnhutchinson.
The function will plot volcano plot together with density of the fold change and p-values on the top and the right side of the volcano plot.
Lorena Pantano, John Hutchinson
1 2 3 4 5 6 |
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