igman: igman

In anastasia-lucas/plotman: A Manhattan Plot Package

Description

Create Interactive Manhattan plots for GWAS

Usage

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

Arguments

d	data frame, must contain SNP, CHR, POS, pvalue columns, optional Shape, Color, and Info
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
db	choose database to connect to ("dbSNP", "GWASCatalog", or enter your own search address)
background	variegated or white
chrblocks	boolean, turns on x-axis chromosome marker blocks
moreinfo	includes more information on hover, refers to Info column
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

html file

See Also

gman, agman, ipheman, ieman

Other GWAS functions: agman, gman

Other interactive plotting functions: ipheman

Examples

data(gwas)
#For this example we will change the "Frame" column to
#"Info" and set the flag moreinfo=TRUE to plot the information
#about the encoding method
colnames(gwas)[5] <- "Info"
igman(d=gwas, line=0.0005, title="GWAS Example", moreinfo=TRUE, db="dbSNP")

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