Yuzhu Chen JL, Yufeng Zhang, Mingqian Zhang, Zheng Sun, Gongchao Jing, Shi Huang , Xiaoquan Su. Parallel-Meta Suite: interactive and rapid microbiome data analysis on multiple platforms. 2022.
https://github.com/qdu-bioinfo/parallel-meta-suite

Instructions

Co-occurrence network mapping using correlations among community members

Read the distance matrix file and construct an undirected graph based on the set threshold and positive and negative edge parameters. Then set the color and weight of the edges in the graph. Positive edges are green, negative edges are red, and based on the absolute value of the correlation coefficient Determine the edge weight. Calculate and visualize various statistical indicators of the network, such as the number of nodes, number of connected components, number of positive and negative edges, network density, diameter, radius and centralization index. The network is laid out using the Fruchterman-Reingold algorithm, and the statistical summary information of the network is used as the title of the figure. Export the network diagram to a PDF file, and indicate the colors of the positive and negative edges in the legend.