Generates a volcano plot using ggplot2

This function generates a base volcanoplot for differentially expressed genes that can then be expanded upon using further ggplot functions.

Usage

de_volcano(
  res_de,
  mapping = "org.Mm.eg.db",
  logfc_cutoff = 0,
  FDR = 0.05,
  draw_FDR_line = FALSE,
  labeled_genes = 30
)

Arguments

res_de

An object containing the results of the Differential Expression analysis workflow (e.g. DESeq2, edgeR or limma). Currently, this can be a DESeqResults object created using the DESeq2 framework.

mapping

Which org.XX.eg.db package to use for annotation - select according to the species

logfc_cutoff

A numeric value that sets the cutoff for the xintercept argument of ggplot. Defaults to 0.

FDR

The pvalue threshold to us for counting genes as de and therefore also where to draw the line in the plot. Default is 0.05

draw_FDR_line

Logical, whether to draw a line at the p-value corresponding to the specified FDR. Defaults to FALSE.

labeled_genes

A numeric value describing the amount of genes to be labeled. This uses the Top(x) highest differentially expressed genes

Value

A ggplot2 volcano plot object that can be extended upon by the user

Examples

library("ggplot2")
library("RColorBrewer")
library("ggrepel")
library("DESeq2")
#> Loading required package: S4Vectors
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#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: Biobase
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library("org.Hs.eg.db")
#> Loading required package: AnnotationDbi
#> 

data(res_de_macrophage, package = "mosdef")

p <- de_volcano(res_macrophage_IFNg_vs_naive,
  logfc_cutoff = 1,
  labeled_genes = 20,
  mapping = "org.Hs.eg.db"
)
#> 'select()' returned 1:many mapping between keys and columns

p
#> Warning: Removed 17787 rows containing missing values or values outside the scale range
#> (`geom_text_repel()`).