Description Usage Arguments Value See Also Examples
Create Manhattan plots for PheWAS
1 2 3 4 5 | pheman(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 = "pheman", hgt = 7,
wi = 12, res = 300)
|
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 0-1, 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 'PHE' or 'Group' column |
background |
variegated or white |
chrblocks |
boolean, turns on x-axis chromosome marker blocks |
file |
file name of saved image |
hgt |
height of plot in inches |
wi |
width of plot in inches |
res |
resolution of plot in pixels per inch |
png image
Other PheWAS functions: apheman
,
ipheman
Other static plotting functions: eman
,
gman
1 2 |
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