agman: agman
In anastasia-lucas/plotman: A Manhattan Plot Package

Description Usage Arguments Value See Also Examples

View source: R/agman.R

Create Manhattan plots for GWAS

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)

`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

gif or mp4 file

gman, igman, apheman, aeman

Other GWAS functions: gman, igman

Other animated plotting functions: aeman, apheman

#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:")