@@ -2,7 +2,7 @@ Package: KEGGlincs

 Type: Package

 Title: Visualize all edges within a KEGG pathway and overlay LINCS data

         [option]

-Version: 1.7.2

+Version: 1.8.1

 Date: 2016-06-02

 Author: Shana White

 Maintainer: Shana White <vandersm@mail.uc.edu>, Mario Medvedovic <medvedm@ucmail.uc.edu>

@@ -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: 6.0.1

+RoxygenNote: 6.1.1

 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

@@ -25,16 +25,13 @@

 #' p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 'HA1E', 

 #'                                data_type = '100_bing', only_mapped = FALSE)

 #'                                

-#' p53_edges_HA1E_ALL <- add_edge_data(p53_edges, p53_KEGG_mappings, 

-#'                                      p53_HA1E_data, c(3, 10,12))

-#' p53_edges_HA1E_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, 

-#'                                         p53_HA1E_data, c(3, 10,12), 

-#'                                         only_mapped = TRUE)

+#' p53_edges_HA1E <- add_edge_data(p53_edges, p53_KEGG_mappings, 

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

 add_edge_data <- function(expanded_edges, KEGG_mappings,

-                          user_data, map_type = "SYMBOL",data_column_no = 3,

-                          only_mapped = FALSE) {

+                          user_data, data_column_no = 3, map_type = "SYMBOL",

+                          only_mapped = TRUE) {

     expanded_edges <- expanded_edges[expanded_edges$type != "maplink", ]

     if (nrow(expanded_edges) > 0) {

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

 \alias{add_edge_data}

 \title{Annotate KEGG edge mappings with user data}

 \usage{

-add_edge_data(expanded_edges, KEGG_mappings, user_data, map_type = "SYMBOL",

-  data_column_no = 3, only_mapped = FALSE)

+add_edge_data(expanded_edges, KEGG_mappings, user_data,

+  data_column_no = 3, map_type = "SYMBOL", only_mapped = TRUE)

 }

 \arguments{

 \item{expanded_edges}{The data frame object generated via the function 

@@ -18,11 +18,11 @@ function expand_KEGG_mappings}

 gene symbols representing an edge and any/all other column[s] contain 

 corresponding edge data.}

+\item{data_column_no}{The column index for desired user data to be added}

+

 \item{map_type}{If the genes in your data set are left untranslated 

 set to "NUMBER" (assuming numbers are gene accession numbers)}

-\item{data_column_no}{The column index for desired user data to be added}

-

 \item{only_mapped}{A logical indicator; if set to FALSE will return 'de-novo'

 edges that 'exist' in data but are not documented in KEGG}

 }

@@ -41,9 +41,6 @@ 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', only_mapped = FALSE)

-p53_edges_HA1E_ALL <- add_edge_data(p53_edges, p53_KEGG_mappings, 

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

-p53_edges_HA1E_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, 

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

-                                        only_mapped = TRUE)

+p53_edges_HA1E <- add_edge_data(p53_edges, p53_KEGG_mappings, 

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

 }

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

 \alias{generate_mappings}

 \title{The 'boilerplate' for this package's desired graph style}

 \usage{

-generate_mappings(style_name, map_edge_width, edge_width_attribute, min_score,

-  max_score)

+generate_mappings(style_name, map_edge_width, edge_width_attribute,

+  min_score, max_score)

 }

 \arguments{

 \item{style_name}{An argument to name style; when used inside 

@@ -4,7 +4,8 @@

 \alias{get_graph_object}

 \title{Generate graph object from nodes and edges}

 \usage{

-get_graph_object(node_mapping_info, expanded_edges, layered_nodes = FALSE)

+get_graph_object(node_mapping_info, expanded_edges,

+  layered_nodes = FALSE)

 }

 \arguments{

 \item{node_mapping_info}{The data.frame object generated by the function