Takes data frame with with an identifier, and two columns of interest to create a beautiful scatter plot, with highlighted gene sets of interest.

ggHighlights(results, x = NULL, y = NULL, genesets = NULL,
  genesets.colors = NULL, genesets.text = NULL,
  gene.identifier = "ENSEMBL", alpha.genesets = 0.7, size.genesets = 2,
  alpha.base = 0.5, size.base = 2, colour.base = "grey60",
  text.size = 4)

Arguments

results

data frame of with an identifier, and two columns of interest

x

x variable (name of column) to plot and any associated transformations

y

y variable (name of column) to plot and any associated transformations

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]

alpha.genesets

alpha value for `geom_point` of genes in genesets

size.genesets

size value for `geom_point` of genesets layer

alpha.base

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

size.base

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

colour.base

colour value for base layer [default: "grey60"]

Value

ggplot2 graphics of volcano plot