hi,everyone, i want to change colors of points log2foldchange>1,but the point it`s y value below 1 can also be changed ,why?

plotMA(x[x$baseMean>1,],col=ifelse(x$log2FoldChange>1,"red","gray"))

Use this

xs <- x[x$baseMean>1, ]
plotMA(xs, col = ifelse(xs$log2FoldChange>1, "red", "gray"))