I'm trying to design an analytics screen where users can compare different aspects of the same data. Is there any evidence that it's easier to compare 2+ charts side-by-side vs. top-to-bottom? Typically, the number of charts should be small enough to fit on the screen in either direction.
Visual analytics works best when all the compared data are within same graph to quick grasp data patterns.
Separating the same data between different charts requires more cognitive load and more complex comparision operations.
Choosing between other options I'll prefer side-by-side one. In case of Y-values (vertical axis) are compared, eye fixes value level at left chart and slides to the right one along imaginary (or real) supported line, see image.
Also you could synchronize the points in different charts according to mouse pointer to provide better orientation between charts. But this requires some interaction programming.
Your question made me think. Showing the graphs side by side or one above the other, will not answer all your queries. You can try intersecting charts.
Like Show two line-charts with different color codes in one single X-Y axis. Or show bar/column charts of different colors and shapes to represent 2 different charts.