R/flow.R

In qgraph: Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation

# flow2 <- function(
#   object, # qgraph object
#   from, # Node of origin
#   horizontal = TRUE,
#   sizeOrig = 10,
#   sizeCon = 3,
#   sizeDiscon = 1,
#   fadingStyle = c("gradual","split","default","off"), # proportional fading to distance?
#   maxFade = 0.25,
#   xScale = 1,
#   ... # Qgraph arguments
# ){
#   fadingStyle <- match.arg(fadingStyle)
#   # Test input:
#   if (!is(object,"qgraph")){
#     warning("Input is not a qgraph object, runnin gqgraph")
#     object <- qgraph(object, ..., DoNotPlot = TRUE)
#   }
#   if (length(from)!=1){
#     stop("'from' must be of length 1")
#   }
#   
#   # Obtain edgelist:
#   E <- as.data.frame(object$Edgelist)
#   
#   # If not fully connected, stop:
#   foo <- capture.output(comps <- sna::components(getWmat(object)))
#   if (comps > 1){
#     stop("Disconnected graph is not yet supported.")
#   }
#   
#   # ID all edges:
#   E$id <- seq_len(nrow(E))
#   
#   # Now we will create new edgelists for every part of the plot. The first will simply connect the target node to its neighbors:
#   flowE <- list()
#   curPart <- 1
#   
#   # Enter the first part (relabel later)
#   part1 <- E[E[,1] == from,c("from","to","weight","id")]
#   part2 <- E[E[,2] == from,c("to","from","weight","id")]
#   names(part2) <- c("from","to","weight","id")
#   flowE[[curPart]] <- rbind(part1,part2)
#   
#   # remaining edges:
#   remainIDs <- E$id[!E$id %in% flowE[[curPart]]$id]
#   
#   # While edges remain, add elements
#   while (length(remainIDs)>0){
#     curPart <- curPart + 1
#     part1 <- E[E[,1] %in% flowE[[curPart-1]]$to,c("from","to","weight","id")]
#     part2 <-  E[E[,2]  %in% flowE[[curPart-1]]$to,c("to","from","weight","id")]
#     names(part2) <- c("from","to","weight","id")
#     flowE[[curPart]] <- rbind(part1,part2)
#     flowE[[curPart]] <- flowE[[curPart]][flowE[[curPart]]$id %in% remainIDs,]
#     
#     # remaining edges:
#     remainIDs <- remainIDs[!remainIDs %in% flowE[[curPart]]$id]
#   }
# 
#   
#   # Now loop over elements to rename nodes:
#   nNodes <- object$graphAttributes$Graph$nNodes
#   allNodes <- seq_len(nNodes)
#   targetNodes <- allNodes[allNodes!=from]
#   nTarget <- length(targetNodes)
#   translateNodes <- NULL
#   for (c in seq_along(flowE)){
#     if (c > 1){
#       flowE[[c]]$from <- translateNodes[match(flowE[[c]]$from ,targetNodes)]
#     } else {
#       flowE[[c]]$from[] <- 1
#     }
#     translateNodes <- 1 + ((c-1) * nTarget) + seq_len(nTarget)
#     flowE[[c]]$to <- translateNodes[match(flowE[[c]]$to ,targetNodes)]
#   }
#   
#   # Compute the layout:
#   L <- matrix(0,1,2)
#   for (c in seq_along(flowE)){
#     L <- rbind(L,
#         cbind(seq(-1,1,length=nTarget),c)
#     )
#   }
# 
#   
#   # Labels:
#   Labels <- object$graphAttributes$Nodes$labels
#   newLabs <- c(Labels[from],rep(Labels[-from],length(flowE)))
#   
#   # Edgelist:
#   flowE <- do.call(rbind,flowE)
#   
#   # Compute sizes:
#   allNodes <- 1:translateNodes[length(translateNodes)]
#   ConnectedNodes <- unlist(flowE[,1:2])
#   vSize <- ifelse(allNodes %in% ConnectedNodes, sizeCon, sizeDiscon)
#   vSize[1] <- sizeOrig
#   
#   # Proportional fading:
#   if (fadingStyle == "default"){
#     Fade <- TRUE
#   } else if (fadingStyle == "off"){
#     Fade <- FALSE
#   } else if (fadingStyle == "gradual"){
#     # Make fading proportional to x location of orin node
#     Fade <- 1-(L[flowE[,1],2]/max(L[flowE[,1],2])  * (1-maxFade))
#   } else {
#     Fade <- ifelse(L[flowE[,1],2]==0,1,maxFade)
#   }
#   
#   # Rescale x:
#   L[,2] <- L[,2]^{1/xScale}
#   
#   # Horizontal:
#   if (horizontal){
#     L <- L[,2:1]
#   }
#   
#   # Plot:
#   qgraph(flowE[,1:3], labels = newLabs, layout = L, directed = FALSE, curve = 0,
#          vsize = vSize, object, DoNotPlot = FALSE,fade=Fade,...)
# }