Pathview now can plot/integrate/compare multiple states/samples or time series in the same graph. Please check Figure 6 - 7 for examples and Subsection 7.2 in the vignette for details. Graphviz view can automatic choose different types of legends, either on nodes (Figure 5b), edges (Figure 2) or both (Figure 3) depending on the specific pathways. These features are available with the latest release of pathview (1.1.7 or newer) and you need to work with BioC 2.13 (current devel version) or newer version: http://bioconductor.org/packages/2.13/bioc/html/pathview.html Thanks for your interest and support. Weijun Luo