ieman: ieman

In anastasia-lucas/plotman: A Manhattan Plot Package

Description

Create interactive Manhattan plots for EWAS

Usage

ieman(d, line, log10 = TRUE, yaxis, ymax, opacity = 1, title = NULL,
  highlight_var, highlight_p, highlighter = "red", color1 = "#AAAAAA",
  color2 = "#4D4D4D", groupcolors, db, moreinfo = FALSE,
  background = "variegated", grpblocks = FALSE, file = "ieman", hgt = 7,
  wi = 12, bigrender = FALSE)

Arguments

d	data frame, columns are Variable, pvalue, and Group; Shape, Color, and Info 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
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
db	query address, ex. "https://www.google.com/search?q="
moreinfo	includes more information on hover, refers to Info 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
bigrender	can set to TRUE for big plots (~50000 rows) that produce huge input lookup error

Value

png image(s)

See Also

eman, aeman, igman, ipheman

Other EWAS functions: aeman, eman

Examples

data(ewas)
ewas$Info <- paste0("Shape: ", ewas$Shape, "\np-value: ", signif(ewas$pvalue, digits=3))
ieman(d=ewas, title="EWAS Example", line=0.001, color1="#A23B72", color2="#2A84AA",
moreinfo=TRUE, highlight_p=0.001, db="https://www.google.com/search?q=", highlighter="green")

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