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 = 1,
  FDR = 0.05,
  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

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

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
#> Loading required package: stats4
#> Loading required package: BiocGenerics
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#> Attaching package: ‘BiocGenerics’
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#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
#>     union, unique, unsplit, which.max, which.min
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
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#> The following objects are masked from ‘package:matrixStats’:
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#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     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
#> Welcome to Bioconductor
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#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
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#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
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#> The following objects are masked from ‘package:matrixStats’:
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#>     anyMissing, rowMedians
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
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead

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