Portfolio analysis of the publication profile of a unit of interest, ranging from individuals and organizations to a scientific field or interdisciplinary programs, aims to inform analysts and decision makers about the position of the unit, where it has been, and where it may go in a complex adaptive environment. A portfolio analysis may aim to identify the gap between the current position of an organization and a goal that it intends to achieve or identify competencies of multiple institutions. We introduce a new visual analytic method for analyzing, comparing, and contrasting characteristics of publication portfolios. The new method introduces a novel design of dual-map thematic overlays on global maps of science. Each publication portfolio can be added as one layer of dual-map overlays over 2 related, but distinct, global maps of science: one for citing journals and the other for cited journals. We demonstrate how the new design facilitates a portfolio analysis in terms of patterns emerging from the distributions of citation threads and the dynamics of trajectories as a function of space and time. We first demonstrate the analysis of portfolios defined on a single source article. Then we contrast publication portfolios of multiple comparable units of interest; namely, colleges in universities and corporate research organizations. We also include examples of overlays of scientific fields. We expect that our method will provide new insights to portfolio analysis.