added dynamic layouts (#23)

NAMESPACE

@@ -3,6 +3,7 @@
 export(annotate_circle)
 export(draw_circle)
 export(layout_as_backbone)
+export(layout_as_dynamic)
 export(layout_igraph_backbone)
 export(layout_igraph_centrality)
 export(layout_igraph_eigen)

R/dynamic_graphs.R

@@ -0,0 +1,89 @@
+#' Dynamic graph layout
+#' @description Layout a series of networks.
+#' @name dynamic_layout
+#' @param gList list of igraph object
+#' @param alpha weighting of reference layout. See details.
+#' @param iter number of iterations during stress optimization
+#' @param tol stopping criterion for stress optimization
+#' @details The reference layout is calculated based on the union of all graphs. The parameter alpha controls the influence of the reference layout.
+#' For alpha=1, only the reference layout is used and all graphs have the same layout. For alpha=0, the stress layout of each individual graph is used. Values inbetween interpolate between the two layouts.
+#' @return coordinates to be used layouting the graphs
+#' @references Brandes, U. and IndleKofer, N. and Mader, M. (2012). Visualization methods for longitudinal social networks and stochastic actor-oriented modeling. *Social Networks* 34 (3) 291-308
+#' @export
+#'
+
+layout_as_dynamic <- function(gList,alpha=0.5,iter=500,tol=0.0001){
+  #prepare reference layout
+  g <- Reduce("%u%",gList)
+  n <- igraph::vcount(g)
+  DList <- lapply(gList,igraph::distances)
+  DList <- adjust_dist(DList)
+  Dmean <- Reduce('+', DList)/length(DList)
+  Dvar <- Reduce('+',lapply(DList, function(x) (x-Dmean)^2))/length(DList)
+  W <- 1/Dmean^2+1/(1+Dvar)
+  diag(W) <- 0
+
+  #calculate reference layout
+  rmat <- matrix(stats::runif(n*2,-0.1,0.1),n,2)
+  xinit <- igraph::layout_with_mds(g) + rmat
+  xref <- stress_major(xinit,W,Dmean,iter,tol)
+
+  xycoords <-vector("list",length(gList))
+  for(i in 1:length(gList)){
+    D <- DList[[i]]
+    W <- 1/D^2
+    diag(W) <- 0
+    if(i==1){
+      xycoords[[i]] <- stress_major(xref,W,D,iter,tol)
+    } else{
+      xycoords[[i]] <- stress_major(xycoords[[i-1]],W,D,iter,tol)
+    }
+    xycoords[[i]] <- (1-alpha)*xycoords[[i]]+alpha*xref
+  }
+  xycoords
+}
+
+adjust_dist <- function(DList){
+  n <- nrow(DList[[1]])
+  for(i in 1:n){
+    for(j in 1:n){
+      for(k in 1:length(DList)){
+        if(is.infinite(DList[[k]][i,j])){
+          lastD <- Inf
+          for(l in seq((k-1),1)){
+            if(l==0){
+              next()
+            }
+            if(!is.infinite(DList[[l]][i,j])){
+              lastD <- DList[[l]][i,j]
+              tlast <- l
+              break()
+            }
+          }
+          nextD <- Inf
+          for(l in seq((k+1),length(DList))){
+            if(l>length(DList)){
+              break()
+            }
+            if(!is.infinite(DList[[l]][i,j])){
+              nextD <- DList[[l]][i,j]
+              tnext <- l
+              break()
+            }
+          }
+          if(!is.infinite(lastD) & !is.infinite(nextD)){
+            beta <- (k-tlast)/(tnext-tlast)
+            DList[[k]][i,j] <- (1-beta)*lastD+beta*nextD+1
+          } else if(is.infinite(lastD) & !is.infinite(nextD)){
+            DList[[k]][i,j] <- nextD+1
+          } else if(!is.infinite(lastD) & is.infinite(nextD)){
+            DList[[k]][i,j] <- lastD+1
+          } else{
+            DList[[k]][i,j] <- sqrt(n)
+          }
+        }
+      }
+    }
+  }
+  DList
+}