The flow lines between different classes are hard for me to see. Is the opacity set based on the total number of particles? Maybe it would be more readable if it were by % of changing particles or relative to the size of each class.
The edges are drawn with line thicknesses proportional to the amount of particles in that connection and normalized wrt the most populous connection (including self connections). Opacity is always 1 (fully opaque), but some lines can appear very faint when their effective thickness is less than 1 pixel. We’re planning on adding some numerical outputs to supplement this visualization, and also adjust for clarity – see this recent discussion with @olibclarke.