eman: eman

In anastasia-lucas/plotman: A Manhattan Plot Package

Description

Create Manhattan plots for EWAS

Usage

eman(d, line, log10 = TRUE, yaxis, ymax, opacity = 1, title = NULL,
  annotate_var, annotate_p, highlight_var, highlight_p, highlighter = "red",
  color1 = "#AAAAAA", color2 = "#4D4D4D", groupcolors,
  background = "variegated", grpblocks = FALSE, file = "eman", hgt = 7,
  wi = 12, res = 300)

Arguments

d	data frame, columns are Variable, pvalue, and Group; Shape and Color optional
line	optional pvalue threshold to draw red line at
log10	plot -log10() of pvalue column, boolean
yaxis	label for y-axis, automatically set if log10=TRUE
ymax	set the upper limit for the y-axis if not automatically scaled
opacity	opacity of points, from 0 to 1, useful for dense plots
title	optional string for plot title
annotate_var	vector of variables to annotate
annotate_p	pvalue threshold to annotate
highlight_var	vector of variables to highlight
highlight_p	pvalue threshold to highlight
highlighter	color to highlight
color1	first alternating color
color2	second alternating color
groupcolors	named vector of colors for data in 'Color' column
background	variegated or white
grpblocks	boolean, turns on x-axis group marker blocks
file	file name of saved image
hgt	height of plot in inches
wi	width of plot in inches
res	resolution of plot in pixels per inch

Value

png image(s)

See Also

ieman, aeman, gman, pheman

Other EWAS functions: aeman, ieman

Other static plotting functions: gman, pheman

Examples

data(ewas)
eman(d=ewas, title="EWAS", line=0.001, annotate_p=0.001, color1="#A23B72", color2="#2A84AA",
highlight_p=0.001, highlighter="green")

anastasia-lucas/plotman documentation built on July 13, 2020, 11:47 p.m.