1. KEGGlincs
  2. Commit 5e82a6eb3b89d2d10c7fcbdc51d089d338192fb6
Browse code

add tidy_edge function

From: Shana White <vandersm@mail.uc.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@130008 bc3139a8-67e5-0310-9ffc-ced21a209358

Shana White authored on 30/05/2017 20:07:01
Showing 5 changed files
NAMESPACE
History View file @ 5e82a6e
... ... 
@@ -16,6 +16,7 @@ export(node_mapping_info)
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 export(overlap_info)
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 export(path_genes_by_cell_type)
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 export(refine_mappings)
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+export(tidy_edge)
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 export(toCytoscape)
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 import(AnnotationDbi)
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 import(KEGGREST)
R/edge_mapping_info.R
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@@ -34,8 +34,9 @@
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 #'
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 edge_mapping_info <-
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-function(expanded_edges, data_added = FALSE, significance_markup = FALSE){
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-    expanded_edges <- expanded_edges[,-c(1)]
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+function(expanded_edges, data_added = FALSE, significance_markup = FALSE,
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+         tidy_edge = TRUE){
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+    #expanded_edges <- expanded_edges[,-c(1)]
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     for(i in 1:nrow(expanded_edges)){
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         if (expanded_edges$subtype1[i] == "activation"){
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             expanded_edges$color[i] = "#b20000"
... ... 
@@ -145,6 +146,27 @@ function(expanded_edges, data_added = FALSE, significance_markup = FALSE){
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             }
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         }
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     }
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-    expanded_edges <- expanded_edges[,c(3:4, 1:2, 5:ncol(expanded_edges))]
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+    #edge_map <- edge_map[,c(2,5,3,1,4:ncol(edge_map))]
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+    expanded_edges<- cbind(expanded_edges[,c("entry1", "entry2","edgeID",
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+                                        "entry1accession", "entry2accession")],
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+                          expanded_edges[,c(6:ncol(expanded_edges))])
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+    expanded_edges <- expanded_edges[order(expanded_edges$edgeID),]
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+
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+    if (tidy_edge == TRUE) {
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+      edge_IDs <- seq(min(expanded_edges$edgeID), max(expanded_edges$edgeID))
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+      for (i in edge_IDs){
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+        if(data_added == TRUE){
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+          expanded_edges <- tidy_edge(edges = expanded_edges,
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+                                      edge_id = edge_IDs[i],
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+                                      data_added = TRUE,
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+                                      by_significance = TRUE)
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+        }
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+        if(data_added == FALSE){
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+          expanded_edges <- tidy_edge(edges = expanded_edges,
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+                                      edge_id = edge_IDs[i],
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+                                      data_added = FALSE)
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+        }
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+      }
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+    }
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     return(expanded_edges)
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 }
R/tidy_edge.R
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new file mode 100644
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@@ -0,0 +1,96 @@
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+#' Tidy up pathway by combining edges inside of edge_mapping_info
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+#' @description Combine edges that share nodes and have other commonalities
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+#' @export
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+#' @param edges The edge dataframe
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+#' @param edge_id The numeric value for the edge_id
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+#' @param by_significance A logical indicator; option if data is added
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+#' @param by_number A logical indicator; gives rough estimate of edge amount
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+#' @return A data frame that has had the given edge condensed for viewing
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+#' @examples \dontrun{
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+#' if (tidy_edge == TRUE) {
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+#'    edge_IDs <- seq(min(expanded_edges$edgeID), max(expanded_edges$edgeID))
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+#'    for (i in edge_IDs){
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+#'      if(data_added == TRUE){
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+#'        expanded_edges <- tidy_edge(edges = expanded_edges,
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+#'                                    edge_id = edge_IDs[i],
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+#'                                    data_added = TRUE,
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+#'                                    by_significance = TRUE)
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+#'      }
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+#'      if(data_added == FALSE){
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+#'        expanded_edges <- tidy_edge(edges = expanded_edges,
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+#'                                    edge_id = edge_IDs[i],
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+#'                                    data_added = FALSE)
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+#'      }
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+#'    }
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+#'
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+#'}
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+#'}
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+
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+tidy_edge <- function(edges, edge_id, data_added = TRUE,
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+                      by_significance = FALSE, by_number = TRUE){
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+  edge <- edges[edges$edgeID == edge_id,]
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+  edges_1 <- edges[edges$edgeID != edge_id,]
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+  if (!data_added){
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+    entry1accessions <- paste(unique(edge$entry1accession), collapse =",")
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+    entry2accessions <- paste(unique(edge$entry2accession), collapse =",")
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+    entry1symbols <- paste(unique(edge$entry1symbol), collapse = ",")
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+    entry2symbols <- paste(unique(edge$entry2symbol), collapse = ",")
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+    tooltip <- paste(entry1symbols, edge$value[1], entry2symbols)
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+    edge$entry1symbol[1] <- entry1symbols
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+    edge$entry2symbol[1] <- entry2symbols
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+    edge$entry1accession[1] <- entry1accessions
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+    edge$entry2accession[1] <- entry2accessions
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+    edge$tooltip[1] <- tooltip
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+    reduced_edge <- edge[1,]
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+  }
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+  if (data_added){
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+    if (sum(edge$has_data) == 0){
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+      entry1accessions <- paste(unique(edge$entry1accession), collapse =",")
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+      entry2accessions <- paste(unique(edge$entry2accession), collapse =",")
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+      entry1symbols <- paste(unique(edge$entry1symbol), collapse = ",")
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+      entry2symbols <- paste(unique(edge$entry2symbol), collapse = ",")
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+      tooltip <- paste(entry1symbols, edge$value[1], entry2symbols)
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+      edge$entry1symbol[1] <- entry1symbols
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+      edge$entry2symbol[1] <- entry2symbols
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+      edge$entry1accession[1] <- entry1accessions
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+      edge$entry2accession[1] <- entry2accessions
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+      edge$tooltip[1] <- tooltip
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+      reduced_edge <- edge[1,]
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+    }
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+
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+    if (sum(edge$has_data) != 0 ){
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+      reduced_edge <- edge[edge$has_data != 0,]
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+      if(by_significance == TRUE){
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+        for (i in 1:length(unique(reduced_edge$color))){
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+          rp <- reduced_edge[reduced_edge$color == unique(reduced_edge$color)[i],]
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+          reduced_edge <- reduced_edge[reduced_edge$color != unique(reduced_edge$color)[i],]
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+          entry1accessions <- paste(unique(rp$entry1accession), collapse =",")
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+          entry2accessions <- paste(unique(rp$entry2accession), collapse =",")
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+          entry1symbols <- paste(unique(rp$entry1symbol), collapse = ",")
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+          entry2symbols <- paste(unique(rp$entry2symbol), collapse = ",")
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+          tooltip <- paste(unique(rp$tooltip), collapse = " , ")
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+          average_summary_score <- mean(rp$summary_score)
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+          rp$entry1symbol[1] <- entry1symbols
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+          rp$entry2symbol[1] <- entry2symbols
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+          rp$entry1accession[1] <- entry1accessions
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+          rp$entry2accession[1] <- entry2accessions
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+          rp$tooltip[1] <- tooltip
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+          rp$summary_score[1] <- average_summary_score
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+
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+          if(by_number == TRUE) {
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+            col <- rp$color[1]
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+            thresh <- min(5, (nrow(rp)-1))
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+            value <- 1-(0.1*thresh)
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+            col1 <- round(value*(col2rgb(col)[1]))
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+            col2 <- round(value*(col2rgb(col)[2]))
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+            col3 <- round(value*(col2rgb(col)[3]))
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+            rp$color[1] <- rgb(col1, col2, col3, maxColorValue = 255)
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+          }
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+          reduced_edge <- rbind(rp[1,], reduced_edge)
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+        }
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+      }
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+    }
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+  }
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+  edges <- rbind (edges_1, reduced_edge)
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+  return(edges)
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+}
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\ No newline at end of file
man/edge_mapping_info.Rd
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... ... 
@@ -5,7 +5,7 @@
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 \title{Prepare edges for mapping}
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 \usage{
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 edge_mapping_info(expanded_edges, data_added = FALSE,
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-  significance_markup = FALSE)
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+  significance_markup = FALSE, tidy_edge = 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
man/tidy_edge.Rd
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new file mode 100644
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@@ -0,0 +1,45 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/tidy_edge.R
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+\name{tidy_edge}
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+\alias{tidy_edge}
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+\title{Tidy up pathway by combining edges inside of edge_mapping_info}
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+\usage{
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+tidy_edge(edges, edge_id, data_added = TRUE, by_significance = FALSE,
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+  by_number = TRUE)
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+}
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+\arguments{
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+\item{edges}{The edge dataframe}
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+
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+\item{edge_id}{The numeric value for the edge_id}
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+
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+\item{by_significance}{A logical indicator; option if data is added}
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+
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+\item{by_number}{A logical indicator; gives rough estimate of edge amount}
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+}
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+\value{
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+A data frame that has had the given edge condensed for viewing
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+}
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+\description{
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+Combine edges that share nodes and have other commonalities
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+}
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+\examples{
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+\dontrun{
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+if (tidy_edge == TRUE) {
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+   edge_IDs <- seq(min(expanded_edges$edgeID), max(expanded_edges$edgeID))
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+   for (i in edge_IDs){
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+     if(data_added == TRUE){
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+       expanded_edges <- tidy_edge(edges = expanded_edges,
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+                                   edge_id = edge_IDs[i],
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+                                   data_added = TRUE,
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+                                   by_significance = TRUE)
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+     }
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+     if(data_added == FALSE){
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+       expanded_edges <- tidy_edge(edges = expanded_edges,
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+                                   edge_id = edge_IDs[i],
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+                                   data_added = FALSE)
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+     }
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+   }
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+
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+}
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+}
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+}