Summary of ggkegg utility. (A) Differentially expressed genes from two different datasets on cellular responses of BK polyomavirus infection in kidney and urothelial cells were identified. Their enriched pathways are shown within a single figure using a scatterpie chart and multiple KEGG PATHWAY networks. The background pie charts represent pathways, and foreground represent in which dataset the genes were significantly differed. The rectangles indicate clusters based on the walktrap graph-based node clustering algorithm. (B) An example of visualizing marker genes for clusters identified in single-cell transcriptomic analysis, based on enrichment analysis of marker genes. The blue color corresponds to the annotation of natural killer cells, the green color represents CD8+ T-cells, and the gold color represents marker genes of both clusters. (C) The analysis of KEGG MODULE completeness based on species-level pangenome information. Microbial gene annotations were obtained for enzyme commission numbers. The numbers were converted to KEGG ORTHOLOGY (KO), and module completeness was computed and visualized by a heatmap. Cell indicates module completeness values, and the row module and the column species. K-means clustering was performed and wordclouds of module description are visualized in the right of the plot. (D) A visualization of log2 fold changes (LFC) of KO on a global metabolic map, identified in the gut metagenomic study of patients with Crohn’s disease. The significantly different KOs were shown, and the node color represents metabolic class and edge colors were based on the LFC of KOs, and the enrichment information of the KEGG PATHWAY is also shown with text, whereby blue represents less abundant and red represents more abundant. The highlighted edges are those related to lipopolysaccharide biosynthesis, and the detail of the pathway is shown in the right plot.