apheman: apheman

In anastasia-lucas/plotman: A Manhattan Plot Package

Description

Create Manhattan plots for PheWAS

Usage

apheman(d, phegroup, line, log10 = TRUE, yaxis, ymax, opacity = 1,
  annotate_snp, annotate_p, highlight_snp, highlight_p, highlighter = "red",
  title = NULL, chrcolor1 = "#AAAAAA", chrcolor2 = "#4D4D4D", groupcolors,
  background = "variegated", chrblocks = TRUE, file = "apheman",
  ext = "gif", hgt = 800, wi = 1300)

Arguments

d	data frame, must contain PHE, SNP, CHR, POS, pvalue, Frame columns, optional Shape
phegroup	optional grouping file for phenotypes, must contain PHE and Group columns
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
annotate_snp	vector of SNPs to annotate
annotate_p	pvalue threshold to annotate
highlight_snp	vector of SNPs to highlight
highlight_p	pvalue threshold to highlight
highlighter	color to highlight
title	optional string for plot title
chrcolor1	first alternating color for chromosome
chrcolor2	second alternating color for chromosome
groupcolors	named vector of colors for data in 'Color' column
background	variegated or white
chrblocks	boolean, turns on x-axis chromosome marker blocks
file	file name of saved image
ext	file type to save, "gif" or "mp4"
hgt	height of plot in pixels
wi	width of plot in pixels

Value

.gif or .mp4 file

See Also

pheman, ipheman, agman, aeman

Other PheWAS functions: ipheman, pheman

Other animated plotting functions: aeman, agman

Examples

#We can duplicate the PHE column so that each
#phenotype will be a frame
data(phewas)
phewas$Frame <- phewas$PHE
apheman(phewas, line=0.001, title="PheWAS Example:")

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