## ----------------------------------------------------------------------------- library(tidyverse) library(ggplot2) library(dce) set.seed(42) ## ----------------------------------------------------------------------------- dce::df_pathway_statistics %>% sample_n(10) %>% arrange(desc(node_num)) %>% 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() ## ----------------------------------------------------------------------------- pathways <- get_pathways( pathway_list = list( kegg = c("Citrate cycle (TCA cycle)") ) ) lapply(pathways, function(x) { plot_network(as(x$graph, "matrix"), visualize_edge_weights = FALSE) + ggtitle(x$pathway_name) }) ## ----------------------------------------------------------------------------- sessionInfo()