Size of points in scatter plot mummichog and GSEA pathway enrichment analysis/ms peaks to pathways

Dear Team,

I was wondering how the size of the points and their colors are calculated when plotting the scatter plot mummichog vs. GSEA?

This is what I found in an article: The color and size of each circle correspond to its p-value and enrichment factor, respectively. Darker tones indicate more statistically relevant predicted pathways. The size of each dot represents the ratio between significant pathway hits and the expected number of compound hits within the pathways.

So does the size now correspond to the combined p-value of GSEA and mummichog? and the color of the points as well?or does the size correspond to the ratio of significant hits and total pathway total?
It is a bit confusing.

Would be very happy if you could help here.

Indeed, the sizes and colors are both based on the combined p value. The ratio is not used here as GSEA is a cutoff-free method - there is no definition of significant hits.

Our documentation is a bit outdated - you can see those details from MetaboAnalystR (if you know R)