phemirror: phemirror

In anastasia-lucas/hudson: A mirrored Manhattan plot package

Description

Create mirrored Manhattan plots for PheWAS Dependencies: ggplot2, gridExtra Suggested: ggrepel

Usage

phemirror(
  top,
  bottom,
  phegroup,
  tline,
  bline,
  chroms = c(1:22, "X", "Y"),
  log10 = TRUE,
  yaxis,
  opacity = 1,
  annotate_snp,
  annotate_p,
  highlight_snp,
  highlight_p,
  highlighter = "red",
  toptitle = NULL,
  bottomtitle = NULL,
  chrcolor1 = "#AAAAAA",
  chrcolor2 = "#4D4D4D",
  groupcolors,
  freey = FALSE,
  background = "variegated",
  chrblocks = TRUE,
  file = "phemirror",
  type = "png",
  hgtratio = 0.5,
  hgt = 7,
  wi = 12,
  res = 300
)

Arguments

top	data frame, must contain PHE, SNP, CHR, POS, pvalue, columns, optional Shape
bottom	data frame, must contain PHE, SNP, CHR, POS, pvalue, columns, optional Shape
phegroup	optional grouping dataframe for phenotypes, must contain PHE and Group columns
tline	list of pvalues to draw red threshold lines in top plot
bline	list of pvalues to draw red threshold lines in bottom plot
chroms	list of chromosomes to plot in the order desired, default c(1:22, "X", "Y")
log10	plot -log10() of pvalue column, logical
yaxis	label for y-axis in the format c("top", "bottom"), automatically set if log10=TRUE
opacity	opacity of points, from 0-1, useful for dense plots
annotate_snp	vector of RSIDs to annotate
annotate_p	list of pvalue thresholds to annotate in the order of c(p_top, p_bottom)
highlight_snp	vector of snps to highlight
highlight_p	list of pvalue thresholds to annotate in the order of c(p_top, p_bottom)
highlighter	color to highlight
toptitle	optional string for top plot title
bottomtitle	optional string for bottom plot title
chrcolor1	first alternating color for chromosome
chrcolor2	second alternating color for chromosome
groupcolors	named vector of colors where names correspond to data in 'PHE' or 'Group' column
freey	allow y-axes to scale with the data
background	variegated or white
chrblocks	logical, turns on x-axis chromosome marker blocks
file	file name of saved image
type	plot type/extension
hgtratio	height ratio of plots, equal to top plot proportion
hgt	height of plot in inches
wi	width of plot in inches
res	resolution of plot in pixels per inch

Value

png image

Examples

data(phewas.t)
data(phewas.b)
phemirror(top=phewas.t, bottom = phewas.b, 
toptitle = "PheWAS Example: Data 1", bottomtitle = "PheWAS Example: Data 2")

anastasia-lucas/hudson documentation built on Nov. 18, 2021, 5:16 p.m.