Interface ThresholdOptions

The significance cutoff on the y axis.

There is deliberately no default. These charts are drawn on transformed axes whose conventions differ by field and by software: -log10(p) at 1.3 for p < 0.05, and at 7.3 for genome-wide significance. A guessed line would sort every point on the figure onto the wrong side, silently.

Which side of the significance cutoff is the significant one.

above is the default because the transformed axes these charts usually carry -- -log10(p) and its relatives -- put the interesting points at the top. A raw p axis runs the other way: there, p <= 0.05 is the finding, and a reading fixed to above would select precisely the points that failed to reach significance and announce them as the result.

That is not a degraded reading, it is the exact inverse of one, which is why this is declarable rather than assumed.

The effect-size cutoff on the x axis, applied to its magnitude -- a volcano is symmetric, and a fold change of -2 is as large an effect as one of +2.