Create volcano plot from log2FC and adjusted pvalues data frame

Create 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)

Arguments

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

Value

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.

Details

This function was mainly developed by @jnhutchinson.

Examples

library(DESeq2)
dds <- makeExampleDESeqDataSet(betaSD = 1)
dds <- DESeq(dds)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
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).