Displaying Variation in Large Datasets: Plotting a Visual Summary of Effect Sizes

Displaying the component-wise between-group differences high-dimensional datasets is problematic because widely used plots such as Bland–Altman and Volcano plots do not show what they are colloquially believed to show. Thus, it is difficult for the experimentalist to grasp why the between-group difference of one component is “significant” while that of another component is not. Here, we propose a type of “Effect Plot” that displays between-group differences in relation to respective underlying variability for every component of a high-dimensional dataset. We use synthetic data to show that such a plot captures the essence of what determines “significance” for between-group differences in each component, and provide guidance in the interpretation of the plot. Supplementary online materials contain the code and data for this article and include simple R functions to produce an effect plot from suitable datasets.