degVolcano.RdCreate volcano plot from log2FC and adjusted pvalues data frame
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 | 
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.
This function was mainly developed by @jnhutchinson.
#>#>#>#>#>#>stats <- results(dds)[,c("log2FoldChange", "padj")] stats[["name"]] <- row.names(stats) degVolcano(stats, plot_text = stats[1:10,])#> Warning: Removed 1 rows containing missing values (geom_text_repel).