## get de score function
getdescore <- function(deseqre,
scoretype = "pval") {
m <- nrow(deseqre)
n <- ncol(deseqre)
if (n == 3) {
deseqre0 <- rep(0, m)
deseqre <- cbind(deseqre, deseqre0)
}
names(deseqre) <- c("name", "pval", "padj", "log2FoldChange")
if (scoretype == "pval") {
descore <- as.numeric(deseqre$pval)
}
if (scoretype == "padj") {
descore <- as.numeric(deseqre$padj)
}
if (scoretype == "log2FoldChange") {
descore <- as.numeric(deseqre$log2FoldChange)
}
dename <- deseqre$name
names(descore) <- as.character(dename)
descore[is.na(descore)] <- 1
if (scoretype != "log2FoldChange") {
descore <- -log10(descore)
}
# de_sig <- descore[descore >= -log10(0.05)]
cf <- quantile(descore, 0.99)
descore[descore > cf] <- cf
return(descore)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.