gg_manhattan: Manhattan plot with ggplot2
In adamleejohnson/r-tools: AJ's R Tools

...

gg_manhattan(
  data,
  chr,
  pos,
  pval,
  label,
  title = NULL,
  label.mode = c("none", "fdr05", "signif", "suggest"),
  label.size = 0.7,
  point.size = 0.8,
  hline.signif = NA,
  hline.suggest = NA,
  highlight_loci.thresh = hline.signif,
  highlight_loci.width = 250,
  highlight_loci.color = "red",
  overplot.limit = 0.05,
  overplot.frac = 0.05,
  chr.colors = manhattan_colors_GnBu(),
  chr.labels = waiver(),
  limits_y = waiver(),
  breaks_y = waiver(),
  progress = TRUE
)

`data`	Input data frame
`chr`	Name of column with chromosome number.
`pos`	Name of column with chromosome position (typically in base pair)
`pval`	Name of column with p-value
`label`	Optional, name of column with rsid symbols, gene symbols, or other labels
`title`	Plot title
`label.mode`	How to apply labels to selected points. One of `c("none", "fdr_0.05", "hline.signif", "hline.suggest")`. `"fdr_0.05"` identifies points that have FDR < 0.05. `"hline.signif"` identifies points above the significance line.
`label.size`	Font size of labels relative to the ggplot theme text element
`point.size`	Size of point. Default 0.8.
`hline.signif`	Horizontal significance line. Can be a number, or "bonferroni" to automatically calculate Bonferroni correction. Use NA to omit.
`hline.suggest`	Horizontal suggestive line. Can be a number, or "bonferroni" to automatically calculate Bonferroni correction. Use NA to omit.
`highlight_loci.thresh`	Threshold p-value to use to identify lead snps in loci that will be highlighted with highlight_loci.color. Use NA to omit.
`highlight_loci.width`	Width, in kilobases, of loci identified by highlight_loci.thresh to include in the highlight regions
`highlight_loci.color`	Highlight color
`overplot.limit`	If there are greater than 1 million points, only a fraction (specified by `overplot.frac`) of the points with p-values above this limit will be randomly removed.
`overplot.frac`	Fraction of points above the overplot.limit to plot. Other points (randomly sampled) will be discarded.
`chr.colors`	Vector of color names, applied to each chromosome.
`chr.labels`	Optional. Chromosome labels.
`limits_y`	Optional. y-axis limits, in -log10 units.
`breaks_y`	Optional. y-axis breaks, in -log10 units.
`progress`	Whether to show a progress bar during ggplot construction