agman: agman

Description Usage Arguments Value See Also Examples

View source: R/agman.R

Description

Create Manhattan plots for GWAS

Usage

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agman(d, 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 = FALSE, file = "agman",
  ext = "gif", hgt = 800, wi = 1300)

Arguments

d

data frame, must contain SNP, CHR, POS, pvalue, Frame columns, optional Shape and Color

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

gman, igman, apheman, aeman

Other GWAS functions: gman, igman

Other animated plotting functions: aeman, apheman

Examples

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#To use the animated plot function, we need to add an animation 'Frame' column to our data
#In this case we will imagine that we've run a GWAS using additive, dominant, and recessive models
#and want to highlight a SNP of interest to see how the p-value changes
data(gwas)
agman(d=gwas, line=0.0005, highlight_snp="rs1777", annotate_snp="rs1777",
highlighter="green", title="GWAS Example:")

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