emirror: emirror

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

Description

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

Usage

emirror(
  top,
  bottom,
  tline,
  bline,
  log10 = TRUE,
  yaxis,
  opacity = 1,
  toptitle = NULL,
  bottomtitle = NULL,
  annotate_var,
  annotate_p,
  highlight_var,
  highlight_p,
  highlighter = "red",
  color1 = "#AAAAAA",
  color2 = "#4D4D4D",
  groupcolors,
  rotatelabels = FALSE,
  labelangle,
  freey = FALSE,
  background = "variegated",
  grpblocks = FALSE,
  file = "emirror",
  type = "png",
  hgtratio = 0.5,
  hgt = 7,
  wi = 12,
  res = 300
)

Arguments

top	data frame, columns one and two must be 'Variable', 'pvalue', and 'Group'; 'Shape' and 'Color' optional
bottom	data frame, columns one and two must be 'Variable', 'pvalue', and 'Group'; 'Shape and 'Color' optional
tline	list of pvalues to draw red threshold lines in top plot
bline	list of pvalues to draw red threshold lines in bottom plot
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 where 0 < opacity <= 1, useful for dense plots
toptitle	optional string for plot title
bottomtitle	optional string for plot title
annotate_var	vector of variable names to annotate
annotate_p	list of pvalue thresholds to annotate in the order of c(p_top, p_bottom)
highlight_var	vector of variables to highlight
highlight_p	list of pvalue thresholds to highlight in the order of c(p_top, p_bottom)
highlighter	color to use for highlight
color1	first alternating color
color2	second alternating color
groupcolors	named vector of colors where names correspond to data in 'Color' column
rotatelabels	logical, rotate axis labels?
labelangle	angle to rotate
freey	allow y-axes to scale with data
background	variegated or white
grpblocks	logical, turns on x-axis group marker blocks
file	file name of saved image
type	plot type/extension, 'pdf' or 'png', etc.
hgtratio	height ratio for top plot; bottom will be auto assigned to 1-hgtratio
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(ewas.t)
data(ewas.b)
emirror(top=ewas.t, bottom=ewas.b, annotate_p = c(0.0001, 0.0005), 
        highlight_p=c(0.0001, 0.0005), highlighter="green", 
        toptitle = "EWAS Comparison Example: Data 1", 
        bottomtitle = "EWAS Comparison Example: Data 2")

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