gg_manhattan: Manhattan plot with ggplot2

In adamleejohnson/R-ajtools: AJ's R Tools

Manhattan plot with ggplot2

Description

...

Usage

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
)

Arguments

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

adamleejohnson/R-ajtools documentation built on April 4, 2022, 7:24 a.m.