Merge pull request #26 from SysBioChalmers/dev

feat: add some description

R/visualization_using_R.R

@@ -2,32 +2,36 @@
 #------------------------------------------------------------------
 # visualization using R platform
 #------------------------------------------------------------------
-# function to define the node in a R graph
+#' function to define the node in a R graph
+#'
+#'
+#' @param rxn_core_carbon_inf a dataframe contains the detailed annotation of rxn_core
+#' @param currency_metabolites_inf a vector of currency metabolites
+#'
+#' @return
+#' @export node_all a dataframe contains the node information for a R graph
+#'
+#' @examples
 creatRnode <- function(rxn_core_carbon_inf, currency_metabolites_inf){
-  #input
-  #rxn_core_carbon_inf a dataframe contains the detailed annotation of rxn_core
-  #currency_metabolites_inf a vector of currency metabolites
-  #output
-  #node_all a dataframe contains the node information for a R graph
-
+
   rxn_core_carbon_inf$rxnID <- str_replace_all(rxn_core_carbon_inf$rxnID, "r_", "R_")
   # analysis the metabolite and remove these currency metabolites
-  # choose the rxn based met 
+  # choose the rxn based met
   met_analysis <- rxn_core_carbon_inf %>%
     count(name) %>%
-    arrange(., desc(n)) 
+    arrange(., desc(n))
   #currency_metabolite_R_map <- c("h", "h2o", "atp", "pi", "adp", "nadp", "nadph", "nad", "nadh",  "ppi",  "amp" )
   met_analysis$name_no_compartment <- str_replace_all(met_analysis$name, "\\[.*?\\]", "")
   met_analysis$currency_sign <- met_analysis$name_no_compartment %in% currency_metabolites_inf
   met_analysis <- filter(met_analysis, currency_sign==FALSE)
-  
-  
+
+
   # define the node
   label_all <- unique(c(rxn_core_carbon_inf$rxnID, met_analysis$name))
   id_all <- 1:length(label_all)
-  
+
   node_all <- data.frame(id=id_all, label=label_all, stringsAsFactors = FALSE)
-  
+
   from0 <- vector()
   to0 <- vector()
   for (i in seq_along(rxn_core_carbon_inf$rxnID)){
@@ -40,19 +44,27 @@ creatRnode <- function(rxn_core_carbon_inf, currency_metabolites_inf){
       to0[i] <- rxn_core_carbon_inf$name[i]
     }
   }
-  
+
   return(node_all)
-  
+
 }
 
-# function to define the edge
+
+
+
+#' function to define the edge
+#'
+#'
+#' @param rxn_core_carbon_inf a dataframe contains the detailed annotation of rxn_core
+#' @param rxn_rev_list a vector contains the reversible reactions
+#' @param node_inf a dataframe contains the node definition for a R graph
+#'
+#' @return
+#' @export edge4 a dataframe defines the edge between the nodes
+#'
+#' @examples
 creatRedge <- function(rxn_core_carbon_inf, rxn_rev_list, node_inf){
-  #input
-  #rxn_core_carbon_inf a dataframe contains the detailed annotation of rxn_core
-  #rxn_rev_list, a vector contains the reversible reactions
-  #node_inf, a dataframe contains the node definition for a R graph
-  #output
-  #edge4, a dataframe defines the edge between the nodes
+
   rxn_core_carbon_inf$rxnID <- str_replace_all(rxn_core_carbon_inf$rxnID, "r_", "R_")
   from0 <- vector()
   to0 <- vector()
@@ -66,9 +78,9 @@ creatRedge <- function(rxn_core_carbon_inf, rxn_rev_list, node_inf){
       to0[i] <- rxn_core_carbon_inf$name[i]
     }
   }
-  
+
   edge0 <- data.frame(from1 = from0, to1 = to0, stringsAsFactors = FALSE)
-  
+
   # add the reversiblity reaction
   rxn_rev <- rxn_rev_list
   edge0$rev_sign1 <- edge0$from1 %in% rxn_rev
@@ -78,25 +90,32 @@ creatRedge <- function(rxn_core_carbon_inf, rxn_rev_list, node_inf){
   edge2_n <- edge2_o
   edge2_n$from1 <- edge2_o$to1
   edge2_n$to1 <- edge2_o$from1
-  
+
   edge3 <- rbind.data.frame(edge0[,1:2], edge2_n)
   edge3$from <- getSingleReactionFormula(node_inf$id,node_inf$label,edge3$from1)
   edge3$to <- getSingleReactionFormula(node_inf$id,node_inf$label,edge3$to1)
-  
+
   edge_all <- edge3[,c('from','to')]
   edge_all$from <- as.numeric(edge_all$from)
   edge_all$to <- as.numeric(edge_all$to)
   return(edge_all)
 }
 
-# function to creat the R graph based on the R platform
+
+
+
+#' function to creat the R graph based on the R platform
+#'
+#'
+#' @param nodes a dataframe contains the id and label information of each node
+#' @param edges a dataframe defining the connection of the metabolite
+#'
+#' @return
+#' @export i_graph_x3 a graph format in R
+#'
+#' @examples
 creatRmap <- function (nodes, edges){
-  # input
-  # nodes, a dataframe contains the id and label information of each node
-  # edges, a dataframe defining the connection of the metabolite
-  # output
-  # i_graph_x3, a graph format in R
-
+
   # Create the graph object
   i_graph_x1 <-
     create_graph()