seekDEvolcano: creates a volcano plot from diff.expr. data
In Solatar/seeqR:

Description Usage Arguments Value Examples

Imports: ggplot2, ggrepel, scales

seekDEvolcano(
  DE,
  genes = NA,
  cutP = 0.05,
  cutFC = 1.5,
  tophitsL = 5,
  tophitsR = 5,
  Title = "",
  textSize = 25,
  labelSize = 7,
  annoSize = 8,
  xLim = c(min(subset(DE, !is.na(padj))$log2FC) - 0.5, max(subset(DE,
    !is.na(padj))$log2FC)) + 0.5,
  yLim = c(min(DE$log10padj), max(DE$log10padj)),
  colors = c("red", "blue", "gray20"),
  lineSize = 1,
  line2Size = 1,
  dotSize = 1,
  dotOpacity = 0.6,
  tickSize = 1,
  annoX = c(2, -2, 0),
  annoY = c(0.1, 0.1, 0.01)
)

`DE`	data.frame with at least 4 columns: Symbol, log2FC, log10padj, color
`genes`	character vector, genes of interest that will have their label shown
`cutP`	number, p value cutoff, will result in a dashed line
`cutFC`	number, fold change cutoff will result in 2 dashed lines (positive and negative cutoff)
`Title`	string, for ggTitle
`textSize`	integer, textsize of title and axis labels
`labelSize`	integer, textsize of individual gene labels
`annoSize`	integer, textsize of the annotation showing the amount of genes for each group
`xLim`	vector of two numbers, limits to the x axis (log2FC). Defaults to the maximum absolute of log2FC expanded by 3 (same value on on each side)
`colors`	vector of strings, determines colors for significant genes 1) up and 2) down, and for 3) unsignificant genes
`lineSize`	number, regulates width of both axis lines
`dotSize`	number, regulates the size of the dots
`dotOpacity`	number between 0 and 1, regulates opacity of dots
`tickSize`	number, regulates width of ticks
`annoX`	vector of numbers, regulates where the annotation for point number is situated on the x axis
`annoY`	vector of numbers, regulates where the annotation for point number is situated on the y axis
`ggplot`	logical, if FALSE, output will be plotly, if TRUE, output will be ggplot2 with labels
`tophits`	either an integer, or the string "custom". If integer, genes with the n-th most positive and n-th most negative log2FC values and/or lowest padj value will be labeled. If "custom", there must already be a column named "tophitsR" and one named "topgitsL".