## ----message=FALSE------------------------------------------------------------ library(tidyverse) library(ggplot2) library(dce) set.seed(42) ## ----------------------------------------------------------------------------- dce::df_pathway_statistics %>% arrange(desc(node_num)) %>% head(10) %>% knitr::kable() ## ----------------------------------------------------------------------------- dce::df_pathway_statistics %>% count(database, sort = TRUE, name = "pathway_number") %>% knitr::kable() ## ----------------------------------------------------------------------------- dce::df_pathway_statistics %>% ggplot(aes(x = node_num)) + geom_histogram(bins = 30) + facet_wrap(~ database, scales = "free") + theme_minimal() ## ----message=FALSE------------------------------------------------------------ pathways <- get_pathways( pathway_list = list( pathbank = c("Lactose Synthesis"), kegg = c("Fatty acid biosynthesis") ) ) lapply(pathways, function(x) { plot_network( as(x$graph, "matrix"), visualize_edge_weights = FALSE, arrow_size = 0.02, shadowtext = TRUE ) + ggtitle(x$pathway_name) }) ## ----------------------------------------------------------------------------- sessionInfo()