phewasManhattan <-
function(d, annotate.phenotype.description=T, ...) {
if(sum(c("phenotype","p") %in% names(d))<2 ) stop("Data input must contain columns phenotype and p.")
if(class(d$phenotype)!="character") {
if(class(d$phenotype)=="factor") {
warning("Factor phenotype input mapped to characters")
d$phenotype=as.character(d$phenotype)
} else {
stop("Non-character or non-factor phenotypes passed in, so an accurate phecode mapping is not possible.")
}
}
#Check to see if it looks 0-padded
if(min(nchar(d$phenotype))<3) warning("Phenotypes with length <3 observed, ensure they are are 0-padded (e.g., \"008\")")
#Add the groups and phecode descriptions as requested
d=addPhecodeInfo(d,groupnums =T, groupcolors = T)
phenotypeManhattan(d, annotate.phenotype.description=annotate.phenotype.description, ...)
}
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