@@ -11,7 +11,7 @@ Description: See what is going on 'under the hood' of KEGG pathways by

         obtained from KGML files.

 License: GPL-3

 LazyData: true

-RoxygenNote: 5.0.1

+RoxygenNote: 6.0.1

 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0)

 SystemRequirements: Cytoscape (>= 3.3.0), Java (>= 8)

 Suggests: BiocInstaller (>= 1.20.3), knitr, graph

@@ -4,7 +4,7 @@

 #' @param pathwayid A KEGG pathway ID of the form "hsa12345" 

 #' (only human pathways currently)

 #' @return A data.frame object with either disease or drug information

-#' @importFrom XML readHTMLTable

+#' @import XML

 #' @export

 #' @examples

 #' RA_drug_table <- get_drug_table("hsa05323")

@@ -69,4 +69,3 @@ p53_edge_info <- KEGG_lincs("hsa04115", graph_title = "p53"

                              convert_KEGG_IDs = FALSE, get_data = TRUE)

                              }

 }

-

@@ -8,4 +8,3 @@

 \description{

 KEGGlincs: an R package designed to explore the edges in KEGG pathways

 }

-

@@ -28,4 +28,3 @@ end_res_edges <- expand_KEGG_edges(end_res_KGML, end_res_KEGG_mappings)

 end_res_drugs <- get_drug_table("hsa01522")

 edges_plus_kdrug <- add_KEGG_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs)

 }

-

@@ -44,4 +44,3 @@ p53_edges_HA1E_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings,

                                         p53_HA1E_data, c(3, 10,12), 

                                         only_mapped = TRUE)

 }

-

@@ -41,5 +41,28 @@ edges <- edge_mapping_info(p53_edges)

 p53_graph_object <- get_graph_object(nodes, edges)

-}

+\dontrun{

+cyto_vis(p53_graph_object, "Default p53 Graph [no data added]")

+

+#Workflow to visualize graph with data-dependent attributes:

+

+p53_KGML <- get_KGML("hsa04115")

+p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)

+nodes <- node_mapping_info(p53_KEGG_mappings)

+p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)

+

+p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, "HA1E", 

+                               data_type = "100_bing")

+p53_edges_plus_data <- add_edge_data(p53_edges, p53_KEGG_mappings, 

+                                      p53_HA1E_data, c(3, 10,12),

+                                      only_mapped = TRUE)

+

+edges <- edge_mapping_info(p53_edges_plus_data, data_added = TRUE)

+                                            

+p53_plus_data_graph_object <- get_graph_object(nodes, edges)

+                                                

+cyto_vis(p53_plus_data_graph_object, "p53 Graph: Mapped Edges + HA1E Data",

+         edge_width_attribute = "UP")

+         }

+}

@@ -48,4 +48,3 @@ p53_edge_mapping_HA1E <- edge_mapping_info(p53_edges_HA1E_data_MAPPED,

                                                       data_added = TRUE)

 }

-

@@ -28,4 +28,3 @@ p53_KGML <- get_KGML("hsa04115")

 p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML, FALSE)

 p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)

 }

-

@@ -31,4 +31,3 @@ mappings based on multi-valued name attribute

 p53_KGML <- get_KGML("hsa04115")

 p53_KEGG_mappings <-  expand_KEGG_mappings(p53_KGML, FALSE)

 }

-

@@ -38,4 +38,3 @@ Intended for use within \code{\link{cyto_vis}}

 style.name = "myKEGGstyle"

 mappings <- generate_mappings(style.name, FALSE)

 }

-

@@ -30,4 +30,3 @@ ribosome_KGML <- get_KGML("hsa03020")

 ribosome_KGML <- get_KGML("hsa03020", get_if_no_edges = TRUE) 

 }

-

@@ -1,8 +1,8 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/get_dd_tables.R

 \name{get_drug_table}

-\alias{get_disease_table}

 \alias{get_drug_table}

+\alias{get_disease_table}

 \title{Import disease/drug tables from KEGG}

 \usage{

 get_drug_table(pathwayid)

@@ -23,4 +23,3 @@ selected pathway

 \examples{

 RA_drug_table <- get_drug_table("hsa05323")

 }

-

@@ -33,4 +33,3 @@ ex.data <- data.frame("UP" = c(70,6), "DOWN" = c(8,20),

 overlaps <- get_fisher_info(ex.data, method = "BH")

 }

-

@@ -42,4 +42,3 @@ layered_nodes_graph_object <- get_graph_object(p53_node_mapping_info,

                                                p53_edge_mapping_info, 

                                                layered_nodes = TRUE)

 }

-

@@ -24,4 +24,3 @@ p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML, FALSE)

 p53_node_mapping_info <- node_mapping_info(p53_KEGG_mappings)

 }

-

@@ -56,4 +56,3 @@ p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings,

                                "HA1E", data_type = "100_bing", 

                                only_mapped = FALSE)

 }

-

@@ -31,4 +31,3 @@ p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)

 path_genes_by_cell_type(p53_KEGG_mappings)

 }

-

@@ -26,4 +26,3 @@ p53_KGML <- get_KGML("hsa04115")

 p53_KEGG_mappings <-  expand_KEGG_mappings(p53_KGML)

 MCF7_p53_mappings <- refine_mappings(p53_KEGG_mappings, "MCF7")

 }

-

@@ -1,8 +1,8 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/from_cyREST.R

 \name{toCytoscape}

-\alias{mapAttributes}

 \alias{toCytoscape}

+\alias{mapAttributes}

 \title{cyREST utility functions}

 \usage{

 toCytoscape(igraphobj)

@@ -26,4 +26,3 @@ A subset of the R utility functions available from/defined

  by cyREST.  The function mapAttributes is called from within toCytoscape 

  which, in turn, is called from within cyto_vis.

 }

-