ipheman: ipheman

In anastasia-lucas/plotman: A Manhattan Plot Package

Description

Create Interactive Manhattan plots for PheWAS

Usage

ipheman(d, phegroup, line, log10 = TRUE, yaxis, ymax, opacity = 1,
  highlight_snp, highlight_p, highlighter = "red", title = NULL,
  chrcolor1 = "#AAAAAA", chrcolor2 = "#4D4D4D", groupcolors,
  background = "variegated", chrblocks = TRUE, db, moreinfo = FALSE,
  bigrender = FALSE, file = "ipheman", hgt = 7, wi = 12)

Arguments

d	data frame, must contain PHE, SNP, CHR, POS pvalue, 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
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
db	choose database to connect to ("dbSNP", "GWASCatalog", or enter your own search address)
moreinfo	includes more information on hover, refers to Info column
bigrender	can set to TRUE for big plots (~50000 rows) that produce huge input lookup error
file	file name of saved image
hgt	height of plot in inches
wi	width of plot in inches

Value

html file

See Also

pheman, apheman, igman, ieman

Other PheWAS functions: apheman, pheman

Other interactive plotting functions: igman

Examples

#In this case we'd like to also see the p-value when we hover over a point,
#so we'll add an 'Info' column to the data
#We'd also like to search dbSNP when we click on a point
data(phewas)
phewas$Info <- paste0("p-value:", signif(phewas$pvalue, digits=3))
ipheman(d=phewas, moreinfo = TRUE, db="dbSNP", line=0.001, title="PheWAS Example")

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