Chapter 10 discusses the use of networks and trees to visualize biological data. It covers the main components of each and how different data sets can be appropriately transformed into specific networks and trees based on what you are trying to present. The vocabulary words for Chapter 10 are:
Graph A structure formed by a set of nodes or vertices and a set of edges between these vertices Adjacency matrix The matrix representation of edges of a graph with as many rows as nodes in the graph Network A weighted, directed graph Sparse In the context of graphs, a term to describe a graph when the number of edges is similar to the number of nodes Dense In the context of graphs, a term to describe a graph when the number of edges is (approximately) a quadratic function of the nodes Arrows/directed edges Graph edges that directionally connect nodes Annotation variables Graph visualization characteristics that help to demonstrate strength of a link in a graph by changing the width of the edge or covariates associated to the size or color of the node Graph layouts Different ways to plot a graph, either for aesthetic or practical reasons Binary data Data in which each observation can take only one of two values (e.