qqmirror: qqmirror

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

Description

Create qqplots with an assumed uniform distribution

Usage

qqmirror(
  top,
  bottom,
  CI = 0.95,
  opacity = 1,
  groupcolors,
  splittop = NULL,
  splitbottom = NULL,
  highlight_p,
  highlight_name,
  annotate_p,
  annotate_name,
  highlighter = "red",
  freey = FALSE,
  tline,
  bline,
  background,
  toptitle = NULL,
  bottomtitle = NULL,
  file = "qqmirror",
  type = "png",
  wi = 6,
  hgt = 8,
  hgtratio = 0.5,
  res = 300
)

Arguments

top	dataframe with at least one column, p-value; Color, Shape, and Name optional
bottom	dataframe with at least one column, p-value; Color, Shape, and Name optional
CI	two-sided confidence interval, default 0.95
opacity	point opacity, default 1
groupcolors	named vector of colors corresponding to data in Group column
splittop	if data contains Color and/or Shape, indicate variable(s) by which the data should be subsetted for calculating CIs
splitbottom	if data contains Color and/or Shape, indicate variable(s) by which the data should be subsetted for calculating CIs
highlight_p	list of pvalue thresholds to highlight in the order of c(p_top, p_bottom)
highlight_name	vector of names to highlight, dataframe must include a Name column
annotate_p	list of pvalue thresholds to annotate in the order of c(p_top, p_bottom)
annotate_name	vector of names to annotate, dataframe must include a Name column to use this option
highlighter	highlighter color
freey	allow y-axes to scale with data
tline	draw a red line at (observed) pvalue threshold in top plot
bline	draw a red line at (observed) pvalue threshold in bottom plot
background	can change to "white"
toptitle	title for top plot
bottomtitle	title for bottom plot
file	filename
type	plot type/extension
wi	width of plot
hgt	height of plot
hgtratio	height ratio for plots
res	resolution of plot

Value

png image

Examples

data(gwas.t)
qqdat <- data.frame(pvalue=gwas.t$pvalue, Color=rep(c("Additive", "Dominant", "Recessive"), 
length.out=nrow(gwas.t), each=1))
qqmirror(top=qqdat, bottom=qqdat, opacity=0.6, splittop="Color", splitbottom="Color", 
toptitle="Example: Top", bottomtitle="Example: Bottom")

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