R/traitsManh.R

In vjcitn/gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

traitsManh = function( gwr, 
   selr=GRanges(seqnames="chr17", IRanges(3e7, 5e7)), 
   traits = c("Asthma", "Parkinson's disease", "Height", "Crohn's disease"),
   truncmlp = 25,
   ...)
 {
 Trait <- NA # try to squelch note
 if (!requireNamespace("ggbio")) stop("install ggbio to use this function")
 gwr = gwr[ which(overlapsAny(gwr, selr)) ]
 availtr = as.character(mcols(gwr)[["DISEASE/TRAIT"]])
 oth = which(!(availtr %in% traits))
 availtr[oth] = "Other"
 mcols(gwr)$Trait = availtr
 pv = mcols(gwr)$PVALUE_MLOG 
 mcols(gwr)$PVALUE_MLOG = ifelse(pv > 25, 25, pv)
 sn = paste(genome(gwr)[1], as.character(seqnames(gwr))[1], sep=" ")
 autoplot(gwr, geom = "point", aes(y = PVALUE_MLOG, color = Trait),
      xlab=sn)

}