## ----render_overview_png,eval=TRUE,echo=FALSE,out.width=800-------------- knitr::include_graphics("image_files/KEGGlincs_overview.jpeg") ## ----initialize, message = FALSE, warning=FALSE-------------------------- library(KEGGlincs) ## ----get_KGML, collapse=TRUE--------------------------------------------- FoxO_KGML <- get_KGML("hsa04068") #Information from KGML can be accessed using the following syntax: slot(FoxO_KGML, "pathwayInfo") ## ----access_KGML, collapse=TRUE------------------------------------------ #Get address for pathway with active links: slot(slot(FoxO_KGML, "pathwayInfo"), "image") ## ----get_png, eval = FALSE----------------------------------------------- # #Download a static pathway image (png file) to working directory: # image_link <- slot(slot(FoxO_KGML, "pathwayInfo"), "image") # download.file(image_link, basename(image_link), mode = "wb") ## ----render_png,eval=TRUE,echo=FALSE,out.width=800----------------------- knitr::include_graphics("image_files/hsa04068.png") ## ----speed_up_for_ex, echo=FALSE----------------------------------------- FoxO_KEGG_mappings <- expand_KEGG_mappings(FoxO_KGML, convert_KEGG_IDs = FALSE) ## ----expand_mapping_for_show, eval=FALSE--------------------------------- # FoxO_KEGG_mappings <- expand_KEGG_mappings(FoxO_KGML) ## ----expand_edges-------------------------------------------------------- FoxO_edges <- expand_KEGG_edges(FoxO_KGML, FoxO_KEGG_mappings) ## ----compare_lengths, collapse=TRUE-------------------------------------- length(graph::nodes(FoxO_KGML)) # 'Un-expanded' nodes nrow(FoxO_KEGG_mappings) # 'Expanded' nodes length(graph::edges(FoxO_KGML)) # 'Un-expanded' edges nrow(FoxO_edges) # 'Expanded' edges ## ----mapping_info, collapse=TRUE----------------------------------------- #Modify existing data sets; specify as nodes and edges FoxO_node_mapping_info <- node_mapping_info(FoxO_KEGG_mappings) FoxO_edge_mapping_info <- edge_mapping_info(FoxO_edges) #Create an igraph object GO <- get_graph_object(FoxO_node_mapping_info, FoxO_edge_mapping_info) class(GO) ## ----cyto_vis, collapse=TRUE, eval=FALSE--------------------------------- # cyto_vis(GO, "FoxO Pathway with Expanded Edges[no data added]") ## ----render_graph,eval=TRUE,echo=FALSE,out.width=800--------------------- knitr::include_graphics("image_files/foxo_ID_conversion.jpeg") ## ----eval = FALSE-------------------------------------------------------- # KEGG_lincs("hsa04068") ## ----eval = FALSE-------------------------------------------------------- # FoxO_edges <- KEGG_lincs("hsa04068") ## ----eval = FALSE, echo = TRUE------------------------------------------- # KEGG_lincs("hsa04068", convert_KEGG_IDs = FALSE) ## ----render_graph_fast,eval=TRUE,echo=FALSE,out.width=800---------------- knitr::include_graphics("image_files/foxo_no_IDconversion.jpeg") ## ----show_KO_data, eval=TRUE,echo=FALSE,out.width=800-------------------- knitr::include_graphics("image_files/random_KO_info.jpeg") ## ----default_p53, eval = FALSE, echo = TRUE------------------------------ # KEGG_lincs("hsa04115") ## ----show_p53_default, eval=TRUE,echo=FALSE,out.width=800---------------- knitr::include_graphics("image_files/p53_default.jpeg") ## ----begin_workflow1----------------------------------------------------- p53_KGML <- get_KGML("hsa04115") p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML) p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings) ## ----show_pathway_genes, eval=FALSE-------------------------------------- # path_genes_by_cell_type(p53_KEGG_mappings) ## ----render_barplot, eval=TRUE,echo=FALSE,out.width=500------------------ knitr::include_graphics("image_files/p53_coverage_graph.png") ## ----show_summary_for_ex, eval = FALSE----------------------------------- # p53_L1000_summary <- path_genes_by_cell_type(p53_KEGG_mappings, get_KOs = TRUE) ## ----avoid_poor_map_render, echo=FALSE----------------------------------- p53_L1000_summary <- path_genes_by_cell_type(p53_KEGG_mappings, get_KOs = TRUE, generate_plot = FALSE) knitr::kable(tail(p53_L1000_summary)) ## ----overlap_info, eval=TRUE, collapse=TRUE------------------------------ p53_PC3_data <- overlap_info(p53_KGML, p53_KEGG_mappings, "PC3") p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, "HA1E") ## ----show_overlap_data, echo = FALSE------------------------------------- knitr::kable(head(p53_PC3_data[1:6])) ## ----overlap_info_plus_genes, eval=TRUE, collapse=TRUE------------------- p53_PC3_data_with_gene_lists <- overlap_info(p53_KGML, p53_KEGG_mappings, "PC3", keep_counts_only = FALSE) ## ----show_overlap_data_plus_genes_PC3, echo = FALSE---------------------- knitr::kable(head(p53_PC3_data_with_gene_lists[c(1:2, 7:10)])) ## ----add_edges----------------------------------------------------------- p53_PC3_edges <- add_edge_data(p53_edges, p53_KEGG_mappings, p53_PC3_data, only_mapped = TRUE, data_column_no = c(3,10,12)) p53_HA1E_edges <- add_edge_data(p53_edges, p53_KEGG_mappings, p53_HA1E_data, only_mapped = TRUE, data_column_no = c(3,10,12)) ## ----get_mapping_info, eval = FALSE-------------------------------------- # p53_node_map <- node_mapping_info(p53_KEGG_mappings) # # p53_edge_map_PC3 <- edge_mapping_info(p53_PC3_edges, data_added = TRUE, # significance_markup = TRUE) # p53_edge_map_HA1E <- edge_mapping_info(p53_HA1E_edges, data_added = TRUE, # significance_markup = TRUE) # # # PC3_GO <- get_graph_object(p53_node_map, p53_edge_map_PC3) # HA1E_GO <- get_graph_object(p53_node_map, p53_edge_map_HA1E) # # cyto_vis(PC3_GO, "Pathway = p53, Cell line = PC3") # #Option: Save PC3 as .cys file and start a fresh session in Cytoscape # cyto_vis(HA1E_GO, "Pathway = p53, Cell line = HA1E") ## ----render_graphs,eval=TRUE,echo=FALSE,out.width=800-------------------- knitr::include_graphics("image_files/p53_PC3_vignette.jpeg") knitr::include_graphics("image_files/p53_HA1E_vignette.jpeg") ## ----auto_map, eval = FALSE---------------------------------------------- # KEGG_lincs("hsa04115", "PC3", refine_by_cell_line = FALSE) # KEGG_lincs("hsa04115", "HA1E", refine_by_cell_line = FALSE) ## ----render_graphs_kegglincs,eval=TRUE,echo=FALSE,out.width=800---------- knitr::include_graphics("image_files/p53_PC3.jpeg") knitr::include_graphics("image_files/p53_HA1E.jpeg")