Browse code

fix add_edge_data, bump version

Shana White authored on 26/03/2019 17:07:42
Showing 5 changed files

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@@ -2,7 +2,7 @@ Package: KEGGlincs
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 Type: Package
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 Title: Visualize all edges within a KEGG pathway and overlay LINCS data
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         [option]
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-Version: 1.7.2
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+Version: 1.8.1
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 Date: 2016-06-02
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 Author: Shana White
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 Maintainer: Shana White <vandersm@mail.uc.edu>, Mario Medvedovic <medvedm@ucmail.uc.edu>
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@@ -11,7 +11,7 @@ Description: See what is going on 'under the hood' of KEGG pathways by
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         obtained from KGML files.
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 License: GPL-3
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 LazyData: true
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-RoxygenNote: 6.0.1
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+RoxygenNote: 6.1.1
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 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0)
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 SystemRequirements: Cytoscape (>= 3.3.0), Java (>= 8)
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 Suggests: BiocInstaller (>= 1.20.3), knitr, graph
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@@ -25,16 +25,13 @@
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 #' p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 'HA1E', 
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 #'                                data_type = '100_bing', only_mapped = FALSE)
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 #'                                
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-#' p53_edges_HA1E_ALL <- add_edge_data(p53_edges, p53_KEGG_mappings, 
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-#'                                      p53_HA1E_data, c(3, 10,12))
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-#' p53_edges_HA1E_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, 
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-#'                                         p53_HA1E_data, c(3, 10,12), 
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-#'                                         only_mapped = TRUE)
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+#' p53_edges_HA1E <- add_edge_data(p53_edges, p53_KEGG_mappings, 
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+#'                                         p53_HA1E_data, c(3, 10,12))
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 add_edge_data <- function(expanded_edges, KEGG_mappings,
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-                          user_data, map_type = "SYMBOL",data_column_no = 3,
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-                          only_mapped = FALSE) {
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+                          user_data, data_column_no = 3, map_type = "SYMBOL",
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+                          only_mapped = TRUE) {
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     expanded_edges <- expanded_edges[expanded_edges$type != "maplink", ]
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     if (nrow(expanded_edges) > 0) {
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@@ -4,8 +4,8 @@
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 \alias{add_edge_data}
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 \title{Annotate KEGG edge mappings with user data}
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 \usage{
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-add_edge_data(expanded_edges, KEGG_mappings, user_data, map_type = "SYMBOL",
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-  data_column_no = 3, only_mapped = FALSE)
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+add_edge_data(expanded_edges, KEGG_mappings, user_data,
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+  data_column_no = 3, map_type = "SYMBOL", only_mapped = TRUE)
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 }
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 \arguments{
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 \item{expanded_edges}{The data frame object generated via the function 
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@@ -18,11 +18,11 @@ function expand_KEGG_mappings}
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 gene symbols representing an edge and any/all other column[s] contain 
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 corresponding edge data.}
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+\item{data_column_no}{The column index for desired user data to be added}
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+
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 \item{map_type}{If the genes in your data set are left untranslated 
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 set to "NUMBER" (assuming numbers are gene accession numbers)}
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-\item{data_column_no}{The column index for desired user data to be added}
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-
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 \item{only_mapped}{A logical indicator; if set to FALSE will return 'de-novo'
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 edges that 'exist' in data but are not documented in KEGG}
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 }
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@@ -41,9 +41,6 @@ p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)
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 p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 'HA1E', 
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                                data_type = '100_bing', only_mapped = FALSE)
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-p53_edges_HA1E_ALL <- add_edge_data(p53_edges, p53_KEGG_mappings, 
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-                                     p53_HA1E_data, c(3, 10,12))
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-p53_edges_HA1E_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, 
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-                                        p53_HA1E_data, c(3, 10,12), 
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-                                        only_mapped = TRUE)
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+p53_edges_HA1E <- add_edge_data(p53_edges, p53_KEGG_mappings, 
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+                                        p53_HA1E_data, c(3, 10,12))
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 }
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@@ -4,8 +4,8 @@
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 \alias{generate_mappings}
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 \title{The 'boilerplate' for this package's desired graph style}
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 \usage{
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-generate_mappings(style_name, map_edge_width, edge_width_attribute, min_score,
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-  max_score)
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+generate_mappings(style_name, map_edge_width, edge_width_attribute,
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+  min_score, max_score)
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 }
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 \arguments{
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 \item{style_name}{An argument to name style; when used inside 
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@@ -4,7 +4,8 @@
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 \alias{get_graph_object}
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 \title{Generate graph object from nodes and edges}
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 \usage{
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-get_graph_object(node_mapping_info, expanded_edges, layered_nodes = FALSE)
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+get_graph_object(node_mapping_info, expanded_edges,
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+  layered_nodes = FALSE)
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 }
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 \arguments{
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 \item{node_mapping_info}{The data.frame object generated by the function