Nothing
genotypePlot <- function(snp,gene,eqtl,geneAnnot=NULL, ylab=NULL, xlab=NULL, mainlab=FALSE){
# First bring the geno objects into the same order as the expression values are...
rowGex <- rownames(eqtl$gex)
takeThese <- is.element(as.character(eqtl$geno$fam[,1]),rowGex)
eqtl$geno$genotypes <- eqtl$geno$genotypes[takeThese,]
eqtl$geno$genotypes <- eqtl$geno$genotypes[order(rowGex),]
snpCol <- which((eqtl$geno$map[,2]==snp)==TRUE)
snpValues <- as.numeric(as.vector(eqtl$geno$genotypes[,snpCol]))
nGroups <- unique(snpValues)
grExpr <- list()
for(i in 1:length(nGroups)){
temp <- rownames(eqtl$geno$genotypes)[snpValues==i]
grExpr[[i]] <- eqtl$gex[is.element(rowGex,temp)]
}
temp <- eqtl$eqtl[names(eqtl$eqtl)==gene]
temp2 <- temp[2]$TestedSNP[,2]==snp
snpP <- temp[3]$p.values[temp2]
if(is.null(geneAnnot)) geneAnnot <- gene
ifelse(mainlab==TRUE, mainTitle <- paste(snp," and ",geneAnnot,". (P-value:",snpP,")",sep=""), mainTitle <- "")
boxplot(grExpr[[1]],xlim=c(0.5,length(grExpr)+0.5),ylim=c(min(as.vector(eqtl$gex)),max(as.vector(eqtl$gex))),main=mainTitle, ylab=ylab, xlab=xlab)
for(i in 2:length(grExpr)){
boxplot(grExpr[[i]],at=i,add=TRUE)
}
# Fill the x-axis
tempRow <- eqtl$geno$map[eqtl$geno$map[,2]==snp,]
al1 <- as.character(tempRow[5])
al2 <- as.character(tempRow[6])
axis(1,at=c(1,2,3),labels=c(paste(al1,"/",al1,sep=""),paste(al1,"/",al2,sep=""),paste(al2,"/",al2,sep="")))
}
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