Description Usage Arguments Value See Also Examples
Create Manhattan plots for GWAS
1 2 3 4 5 |
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
Other GWAS functions: gman
,
igman
Other animated plotting functions: aeman
,
apheman
1 2 3 4 5 6 | #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:")
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