test_sup_nodes = function() { # devtools::load_all() dirpath = system.file('data', package = 'kgraph') pval <- readRDS(file.path(dirpath, "pval.rds")) %>% as.data.frame #dict <- readRDS(file.path(dirpath, "df_dict_dg.rds")) %>% as.data.frame df_dict <- get(load(file.path(dirpath, "df_dict_dg.rds"))) #df_drugs = data.table::fread(file.path(dirpath, 'drug_gene_phase_v32_17APR2024.csv'), data.table = FALSE) #df_pheno = subset(dict, dataset %in% c('Labs', 'Others', 'PheCodes', 'Vital Signs')) #df_gene = subset(dict, dataset == 'GENE') #df_dict = rbind(df_pheno, df_gene) # df_gene %<>% druggablegenome:::add_drug_info(df_drugs) # df_drugs = subset(df_gene, !is.na(drug_name)) #df_gene = get(load(file.path(dirpath, 'df_gene.rds'))) df_drugs = get(load(file.path(dirpath, 'df_drugs.rds'))) pval$PVAL = -log10(pval$PVAL) df_weights = pval %>% setNames(c('concept1', 'concept2', 'weight')) col_idx = match('type_color', names(df_dict)) names(df_dict)[col_idx] = 'color' selected_phenos = c('Bicarbonate_Max', 'Chloride_BSP_Max') l_graph = kgraph:::build_kgraph(selected_phenos, df_weights, df_dict, spring_weights = TRUE, exp_scale = 15, display_val_str = '\nP-value: ', str_other = 'Other gene', lower_bound_const = 3) l_graph = kgraph:::build_kgraph(selected_phenos, df_weights, df_dict, df_sup_nodes = df_drugs, spring_weights = TRUE) igraph = sgraph:::l_graph_to_igraph(l_graph) sgraph = sgraph:::sgraph_clusters(igraph, node_size = 'weight', label = label_attrs, layout = igraph::layout_with_kk(igraph)) expect_true(TRUE) # test_groups = function() { # FIXME # linked to both Other and to group (i think it's resolved now) l_graph$df_links %>% subset(to == 'AS3MT') } #test_that('sup_nodes', test_sup_nodes())