... | ... |
@@ -2,7 +2,7 @@ Package: KEGGlincs |
2 | 2 |
Type: Package |
3 | 3 |
Title: Visualize all edges within a KEGG pathway and overlay LINCS data |
4 | 4 |
[option] |
5 |
-Version: 1.7.2 |
|
5 |
+Version: 1.8.1 |
|
6 | 6 |
Date: 2016-06-02 |
7 | 7 |
Author: Shana White |
8 | 8 |
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 |
11 | 11 |
obtained from KGML files. |
12 | 12 |
License: GPL-3 |
13 | 13 |
LazyData: true |
14 |
-RoxygenNote: 6.0.1 |
|
14 |
+RoxygenNote: 6.1.1 |
|
15 | 15 |
Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) |
16 | 16 |
SystemRequirements: Cytoscape (>= 3.3.0), Java (>= 8) |
17 | 17 |
Suggests: BiocInstaller (>= 1.20.3), knitr, graph |
... | ... |
@@ -25,16 +25,13 @@ |
25 | 25 |
#' p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 'HA1E', |
26 | 26 |
#' data_type = '100_bing', only_mapped = FALSE) |
27 | 27 |
#' |
28 |
-#' p53_edges_HA1E_ALL <- add_edge_data(p53_edges, p53_KEGG_mappings, |
|
29 |
-#' p53_HA1E_data, c(3, 10,12)) |
|
30 |
-#' p53_edges_HA1E_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, |
|
31 |
-#' p53_HA1E_data, c(3, 10,12), |
|
32 |
-#' only_mapped = TRUE) |
|
28 |
+#' p53_edges_HA1E <- add_edge_data(p53_edges, p53_KEGG_mappings, |
|
29 |
+#' p53_HA1E_data, c(3, 10,12)) |
|
33 | 30 |
|
34 | 31 |
|
35 | 32 |
add_edge_data <- function(expanded_edges, KEGG_mappings, |
36 |
- user_data, map_type = "SYMBOL",data_column_no = 3, |
|
37 |
- only_mapped = FALSE) { |
|
33 |
+ user_data, data_column_no = 3, map_type = "SYMBOL", |
|
34 |
+ only_mapped = TRUE) { |
|
38 | 35 |
|
39 | 36 |
expanded_edges <- expanded_edges[expanded_edges$type != "maplink", ] |
40 | 37 |
if (nrow(expanded_edges) > 0) { |
... | ... |
@@ -4,8 +4,8 @@ |
4 | 4 |
\alias{add_edge_data} |
5 | 5 |
\title{Annotate KEGG edge mappings with user data} |
6 | 6 |
\usage{ |
7 |
-add_edge_data(expanded_edges, KEGG_mappings, user_data, map_type = "SYMBOL", |
|
8 |
- data_column_no = 3, only_mapped = FALSE) |
|
7 |
+add_edge_data(expanded_edges, KEGG_mappings, user_data, |
|
8 |
+ data_column_no = 3, map_type = "SYMBOL", only_mapped = TRUE) |
|
9 | 9 |
} |
10 | 10 |
\arguments{ |
11 | 11 |
\item{expanded_edges}{The data frame object generated via the function |
... | ... |
@@ -18,11 +18,11 @@ function expand_KEGG_mappings} |
18 | 18 |
gene symbols representing an edge and any/all other column[s] contain |
19 | 19 |
corresponding edge data.} |
20 | 20 |
|
21 |
+\item{data_column_no}{The column index for desired user data to be added} |
|
22 |
+ |
|
21 | 23 |
\item{map_type}{If the genes in your data set are left untranslated |
22 | 24 |
set to "NUMBER" (assuming numbers are gene accession numbers)} |
23 | 25 |
|
24 |
-\item{data_column_no}{The column index for desired user data to be added} |
|
25 |
- |
|
26 | 26 |
\item{only_mapped}{A logical indicator; if set to FALSE will return 'de-novo' |
27 | 27 |
edges that 'exist' in data but are not documented in KEGG} |
28 | 28 |
} |
... | ... |
@@ -41,9 +41,6 @@ p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings) |
41 | 41 |
p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 'HA1E', |
42 | 42 |
data_type = '100_bing', only_mapped = FALSE) |
43 | 43 |
|
44 |
-p53_edges_HA1E_ALL <- add_edge_data(p53_edges, p53_KEGG_mappings, |
|
45 |
- p53_HA1E_data, c(3, 10,12)) |
|
46 |
-p53_edges_HA1E_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, |
|
47 |
- p53_HA1E_data, c(3, 10,12), |
|
48 |
- only_mapped = TRUE) |
|
44 |
+p53_edges_HA1E <- add_edge_data(p53_edges, p53_KEGG_mappings, |
|
45 |
+ p53_HA1E_data, c(3, 10,12)) |
|
49 | 46 |
} |
... | ... |
@@ -4,8 +4,8 @@ |
4 | 4 |
\alias{generate_mappings} |
5 | 5 |
\title{The 'boilerplate' for this package's desired graph style} |
6 | 6 |
\usage{ |
7 |
-generate_mappings(style_name, map_edge_width, edge_width_attribute, min_score, |
|
8 |
- max_score) |
|
7 |
+generate_mappings(style_name, map_edge_width, edge_width_attribute, |
|
8 |
+ min_score, max_score) |
|
9 | 9 |
} |
10 | 10 |
\arguments{ |
11 | 11 |
\item{style_name}{An argument to name style; when used inside |
... | ... |
@@ -4,7 +4,8 @@ |
4 | 4 |
\alias{get_graph_object} |
5 | 5 |
\title{Generate graph object from nodes and edges} |
6 | 6 |
\usage{ |
7 |
-get_graph_object(node_mapping_info, expanded_edges, layered_nodes = FALSE) |
|
7 |
+get_graph_object(node_mapping_info, expanded_edges, |
|
8 |
+ layered_nodes = FALSE) |
|
8 | 9 |
} |
9 | 10 |
\arguments{ |
10 | 11 |
\item{node_mapping_info}{The data.frame object generated by the function |