## ---- echo = FALSE-------------------------------------------------------------------------------- library(knitr) knitr::opts_chunk$set( error = FALSE, tidy = FALSE, message = FALSE, warning = FALSE, fig.align = "center", dev = "jpeg" ) options(width = 100) ## ---- echo = FALSE, message = FALSE--------------------------------------------------------------- library(simplifyEnrichment) mat = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds", package = "simplifyEnrichment")) go_id = rownames(mat) ## ---- eval = FALSE-------------------------------------------------------------------------------- # library(simplifyEnrichment) # set.seed(888) # go_id = random_GO(500) ## ---- eval = FALSE-------------------------------------------------------------------------------- # mat = GO_similarity(go_id) ## ---- eval = FALSE-------------------------------------------------------------------------------- # GO_similarity(go_id, measure = "Wang") ## ---- fig.width = 7*1.2, fig.height = 4*1.2------------------------------------------------------- df = simplifyGO(mat) ## ------------------------------------------------------------------------------------------------- head(df) ## ------------------------------------------------------------------------------------------------- sort(table(df$cluster)) ## ---- eval = FALSE-------------------------------------------------------------------------------- # split(df, df$cluster) ## ------------------------------------------------------------------------------------------------- binary_cut(mat) ## ---- eval = FALSE-------------------------------------------------------------------------------- # cluster_terms(mat, method = "binary_cut") ## ---- fig.width = 10, fig.height = 7-------------------------------------------------------------- compare_clustering_methods(mat) ## ---- fig.width = 18, fig.height = 14, dev = "jpeg"----------------------------------------------- compare_clustering_methods(mat, plot_type = "heatmap") ## ---- eval = FALSE-------------------------------------------------------------------------------- # set.seed(123) # compare_clustering_methods(mat) # set.seed(123) # compare_clustering_methods(mat, plot_type = "heatmap") ## ---- eval = FALSE-------------------------------------------------------------------------------- # clt = cmp_make_clusters(mat) # just a list of cluster labels # cmp_make_plot(mat, clt) # cmp_make_plot(mat, clt, plot_type = "heatmap") ## ---- eval = FALSE-------------------------------------------------------------------------------- # register_clustering_methods( # method1 = function(mat, ...) ..., # method2 = function(mat, ...) ..., # ... # ) ## ------------------------------------------------------------------------------------------------- sessionInfo()