Takes data frame with log2FoldChange and padj values and gene symbols to create a beautiful volcano plot, with highlighted gene sets of interest. If a padj is set to NA, it will take on the minimum value found in the data.

ggVolcanos(results, genesets = NULL, genesets.colors = NULL,
  genesets.text = NULL, gene.identifier = "ENSEMBL", padj.threshold = 0.1,
  lfc.threshold = log2(1.5), alpha.base = 0.5, alpha.genesets = 0.7,
  colour.base = "grey60", text.size = 4)

Arguments

results

data frame of expression values with columns `log2FoldChange` and `padj` (as in DESeq2 output) and `gene_id` if you are using the genesets argument.

genesets

named list containing geneset(s) to highlight/label

genesets.colors

vector of colors to correspond to each geneset list must be the same order as genesets

genesets.text

character vector of genes to label with text

gene.identifier

column to be used for highlighting/genesets (default uses ENSEMBL column) [unused; needed for flexible gene_id labeling]

padj.threshold

significance threshold for padj values

lfc.threshold

significance threshold for log2FoldChange values

alpha.base

alpha value for `geom_point` of baselayer (non-geneset genes)

alpha.genesets

alpha value for `geom_point` of genes in genesets

text.size

size of labels for text layer

Value

ggplot2 graphics of volcano plot

Examples

ggVolcanos(results, c(TE = "Tbx21", MP = "Tcf7"))

genesets.colors = c(MP = "blue", TE = "red")nnn
genesets <- list(MP = c("Tcf7", "Il7r"), TE = c("Gzmb", "Klrg1"))
ggVolcanos(results, genesets, genesets.colors)