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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.

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As Aryan Vijay implies below, the answer to your question depends on the type of chart, the data, and the type of comparison. Can you be more specific about any of these three factors? Also, search for 'trellis chart', 'scatterplot matrix', or 'small multiples' to see standard ways of arranging charts for comparison across charts. – user1757436 Sep 6 '13 at 20:05

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.

enter image description here

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. enter image description here

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. enter image description here

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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.

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