In this study, we examine two algorithms for visualizing and comparing transition probability matrices: ordered semantic co-registration layout (OSC) and modified dot layout (MDL). We examine how each algorithm utilizes key visual channels—position, shape, size, and color—in network layouts and encodings. Our findings show that for layouts, OSC provides consistent node positioning that reflects key group characteristics, which facilitates easier comparisons across networks. In contrast, MDL’s inconsistent node placement across groups makes it harder to compare networks visually. For encodings, OSC uses high-discriminability shapes and colors to encode node and edge weights, while MDL’s reliance on black lines and label-length-based node sizes limits its ability to visually distinguish weights. We conclude that OSC is more suited for comparing multiple transition probability matrices with a small number of nodes, while MDL may perform better in larger networks.