authors, citation, doc fixes

DESCRIPTION

@@ -1,7 +1,11 @@
 Package: gatom
 Title: Finding an Active Metabolic Module in Atom Transition Network
 Version: 0.99.0
-Authors@R: person("Alexey", "Sergushichev", email = "[email protected]", role = c("aut", "cre"))
+Authors@R: 
+    c(
+    person("Anastasiia", "Gainullina", role = c("aut")),
+    person("Mariia", "Emelianova", role = c("aut")),
+    person("Alexey", "Sergushichev", email = "[email protected]", role = c("aut", "cre")))
 Description: This package implements a metabolic network analysis pipeline to 
     identify an active metabolic module based on high throughput data. 
     The pipeline takes as input transcriptional and/or metabolic data 

R/gatom.R

@@ -265,7 +265,7 @@ makeMetabolicGraph <- function(network,
 #' @import BioNet
 #' @importFrom mwcsr normalize_sgmwcs_instance
 #'
-#' @return scored igraph object
+#' @return SGMWCS instance or scored igraph object
 #'
 #' @examples
 #' data("gEx")

R/io.R

@@ -5,7 +5,7 @@
 #' @param n_iter Number of repel algorithm iterations
 #' @param force Value of repel force
 #'
-#' @return NULL
+#' @return Returns NULL
 #'
 #' @examples
 #' data(mEx)
@@ -197,7 +197,7 @@ sanitizeForXml <- function (string) {
 #' @param file File to save to
 #' @param name Name of the module
 #'
-#' @return NULL
+#' @return Returns NULL
 #'
 #' @examples
 #' data(mEx)
@@ -340,7 +340,7 @@ getEdgeXmlStrings <- function(module, indent="") {
 #' @param extra.node.attrs Table with additional node attributes to be written to the dot file as is
 #' @param extra.edge.attrs Table with additional edge attributes to be written to the dot file as is
 #'
-#' @return NULL
+#' @return Returns NULL
 #'
 #' @examples
 #' data(mEx)
@@ -530,7 +530,7 @@ getEdgeDotStrings <- function(module, indent="", extra.attrs=NULL) {
 #' @param sizingPolicy A widget sizing policy
 #' @param ... Other parameters
 #'
-#' @return NULL
+#' @return Returns NULL
 #'
 #' @examples
 #' data(mEx)

inst/CITATION

@@ -0,0 +1,21 @@
+citHeader("To cite gatom in publications use:")
+
+citEntry(
+  entry    = "Article",
+  title    = "Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks",
+  author   =     c(
+    person("Mariia", "Emelianova"),
+    person("Anastasiia", "Gainullina"),
+    person("Nikolay", "Poperechnyi"),
+    person("Alexander", "Loboda"),
+    person("Maxim", "Artyomov"),
+    person("Alexey", "Sergushichev")),
+  journal  = "Nucleic Acids Research",
+  year     = "2022",
+  volume   = "50",
+  number   =  "W1",
+  pages    =  "W690-W696",
+  url      = "https://doi.org/10.1093/nar/gkac427",
+  textVersion = paste("Mariia Emelianova, Anastasiia Gainullina, Nikolay Poperechnyi, Alexander Loboda, Maxim Artyomov, Alexey Sergushichev, Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W690-W696, https://doi.org/10.1093/nar/gkac427"
+  )
+)