Description Usage Arguments Value See Also Examples
Create Interactive Manhattan plots for PheWAS
1 2 3 4 5 | ipheman(d, phegroup, line, log10 = TRUE, yaxis, ymax, opacity = 1,
highlight_snp, highlight_p, highlighter = "red", title = NULL,
chrcolor1 = "#AAAAAA", chrcolor2 = "#4D4D4D", groupcolors,
background = "variegated", chrblocks = TRUE, db, moreinfo = FALSE,
bigrender = FALSE, file = "ipheman", hgt = 7, wi = 12)
|
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 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 |
background |
variegated or white |
chrblocks |
boolean, turns on x-axis chromosome marker blocks |
db |
choose database to connect to ("dbSNP", "GWASCatalog", or enter your own search address) |
moreinfo |
includes more information on hover, refers to Info column |
bigrender |
can set to TRUE for big plots (~50000 rows) that produce huge input lookup error |
file |
file name of saved image |
hgt |
height of plot in inches |
wi |
width of plot in inches |
html file
Other PheWAS functions: apheman
,
pheman
Other interactive plotting functions: igman
1 2 3 4 5 6 | #In this case we'd like to also see the p-value when we hover over a point,
#so we'll add an 'Info' column to the data
#We'd also like to search dbSNP when we click on a point
data(phewas)
phewas$Info <- paste0("p-value:", signif(phewas$pvalue, digits=3))
ipheman(d=phewas, moreinfo = TRUE, db="dbSNP", line=0.001, title="PheWAS Example")
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