R/treeAndLeaf.R

In TreeAndLeaf: An alternative to dendrogram visualization and insertion of multiple layers of information

#' Layout creation and plotting of the TreeAndLeaf in RedeR.
#'
#' Creates tree-and-leaf layouts and plots. It also returns the given igraph
#' with nodes coordinates added after setting of positions and relaxation by
#' the force based algorithm implemented in the RedeR package.
#'
#' @param obj An object of RedPort class, from RedeR package <RedPort>.
#' @param gg An igraph object generated by either \code{\link{hclust2igraph}}
#' or \code{\link{phylo2igraph}}<igraph>.
#' 
#' @return Plotting of igraph in RedeR app and the given igraph with nodes
#' coordinates added.
#'
#' @seealso \code{\link{formatTree}}
#' @seealso \code{\link[RedeR:addGraph]{addGraph}}
#' @seealso \code{\link[RedeR:relax]{relax}}
#'
#' @examples
#' library(RedeR)
#' rdp <- RedPort()
#' hc <- hclust(dist(USArrests), "ave")
#' gg <- hclust2igraph(hc)
#' 
#' \dontrun{
#' calld(rdp)
#' treeAndLeaf(rdp, gg)
#' }
#' 
#' @importFrom methods is 
#' @importFrom igraph get.edgelist V vcount is.igraph
#' @importFrom RedeR .rederpost addGraph relax getGraph RedPort
#' @export


treeAndLeaf <- function(obj, gg){
    
    #-- Checks
    tal.checks(name = "obj", para = obj)
    tal.checks(name = "gg", para = gg)
    #Size determination based on number of leaves
    sz <- length(igraph::V(gg)$name) - length(gg$intnodes)
    if(sz <= 100){ 
        size <- "small"
    } else if(sz >100 && sz <= 250){
        size <- "medium"
    } else {
        size<-"large"
    }
    #-- Find root and get number of leafs
    edgelist <- igraph::get.edgelist(gg)
    root <- .findRoot(edgelist)
    #-- Start layout
    layout <- matrix(0, nrow = igraph::vcount(gg), ncol = 2,
                     dimnames = list(igraph::V(gg)$name, c("x","y")))
    #-- Calculate the edges lengths for root
    elL <- .findSubTreeSizeLeft(root, edgelist)*10
    elR <- .findSubTreeSizeRight(root, edgelist)*10
    #-- Find the root's children from edgelist
    children <- edgelist[which(edgelist[,1] %in% root),2]
    #-- Set the layout
    layout[children[1],] <- c(elR, 0)
    layout[children[2],] <- c(-elL, 0)
    TaL <- new.env(parent = emptyenv())
    assign("count", 0, envir = TaL)
    #-- Recursively set the layout for the rest of the binary tree
    layout <- .setLayout(children[1], edgelist, layout, size = size, TaL = TaL)
    layout <- .setLayout(children[2], edgelist, layout, size = size, TaL = TaL)
    gg <- .showGraph(obj, gg, layout, size)
    rm(TaL)
    return(invisible(gg))
}

.showGraph <- function(obj, gg, layout, size){
    if(!is.null(igraph::V(gg)$nodeSize)){
        gg2 <- .normggSize(gg, 50, 200)
    } else {
        gg2 <- gg
    }
    RedeR::.rederpost(obj, 'RedHandler.stopPaint')
    switch(size,
           small = suppressMessages(RedeR::addGraph(obj, gg2, layout = layout,
                                                    zoom = 14)),
           medium = suppressMessages(RedeR::addGraph(obj, gg2, layout = layout,
                                                     zoom = 7)),
           large = suppressMessages(RedeR::addGraph(obj, gg2, layout = layout,
                                                    zoom = 3)))
    switch(size,
           small = RedeR::relax(obj, p1 = 50, p8 = 40, ps = TRUE, p9 = 10000),
           medium = RedeR::relax(obj, p1 = 80, p2 = 120, p5 = 500, p8 = 60,
                                 ps = TRUE, p9 = 10000),
           large = RedeR::relax(obj, p1 = 100, p2 = 150, p5 = 500, p8 = 80,
                                ps = TRUE, p9 = 10000))
    
    seconds <- ceiling(length(igraph::V(gg)$name)/25)+2
    message("Please wait... Your tree will be available in ", seconds,
            " seconds.")
    Sys.sleep(seconds)
    switch(size,
           small = suppressMessages(RedeR::addGraph(obj, gg, layout = NULL,
                                                    zoom = 14)),
           medium = suppressMessages(RedeR::addGraph(obj, gg, layout = NULL,
                                                     zoom = 7)),
           large = suppressMessages(RedeR::addGraph(obj, gg, layout = NULL,
                                                    zoom = 2)))
    switch(size,
           small = RedeR::relax(obj, p1 = 50, p8 = 40, ps = TRUE, p9 = 10000),
           medium = RedeR::relax(obj, p1 = 60, p5 = 100, p8 = 60, ps = TRUE,
                                 p9 = 10000),
           large = RedeR::relax(obj, p1 = 80, p2 = 50, p5 = 100, p8 = 100,
                                ps = TRUE, p9 = 10000))
    Sys.sleep(1)
    RedeR::.rederpost(obj, 'RedHandler.startPaint')
    gg3 <- RedeR::getGraph(obj, attribs = "all")
    return(invisible(gg3))
}

.setLayout <- function(node, edgelist, layout, size = "small", TaL){
    if(node %in% edgelist[,1]){
        #-- Counter to alternate between directions
        assign("count", get("count", envir = TaL)+1, envir = TaL)
        #-- Find children
        children <- edgelist[which(edgelist[,1] %in% node),2]
        #-- Calculate edges
        if(size == "small"){
            elL <- (.findSubTreeSizeLeft(node, edgelist)*10)
            elR <- (.findSubTreeSizeRight(node, edgelist)*10)
        }
        if(size == "medium"){
            elL <- (.findSubTreeSizeLeft(node, edgelist)*10 +
                        .countChildren(node, edgelist)*5)
            elR <- (.findSubTreeSizeRight(node, edgelist)*10 +
                        .countChildren(node, edgelist)*5)
        }
        if(size == "large"){
            elL <- (.findSubTreeSizeLeft(node, edgelist)*10 +
                        .countChildren(node, edgelist)*10)
            elR <- (.findSubTreeSizeRight(node, edgelist)*10 +
                        .countChildren(node, edgelist)*10)
        }
        #-- Alternates between up/down and left/right
        if(get("count", envir = TaL) %% 3 == 0){
            coord.child1 <- c(layout[node, 1], layout[node, 2] + elR)
            coord.child2 <- c(layout[node, 1], layout[node, 2] - elL)
        }
        if(get("count", envir = TaL) %% 3 == 1){
            coord.child1 <- c(layout[node, 1] + elR, layout[node, 2])
            coord.child2 <- c(layout[node, 1] - elL, layout[node, 2])
        }
        if(get("count", envir = TaL) %% 3 == 2){
            coord.child1 <- c(layout[node, 1] + 0.5*elR,
                              layout[node, 2]+ 0.5*elR)
            coord.child2 <- c(layout[node, 1] - 0.5*elL,
                              layout[node, 2]- 0.5*elL)
        }
        #-- Set the layout
        layout[children[1],] <- coord.child1
        layout[children[2],] <- coord.child2
        #-- Recursive call
        layout <- .setLayout(children[1], edgelist, layout, size, TaL = TaL)
        layout <- .setLayout(children[2], edgelist, layout, size, TaL = TaL)
    } else {
        return(layout)
    }
}

.findSubTreeSizeLeft <- function(node, edgelist, length = 0){
    children <- edgelist[which(edgelist[,1] %in% node),2]
    if(node %in% edgelist[,1]){
        length <- length + 1
        length <- .findSubTreeSize(children[2], edgelist, length)
    }
    return(length)
}

.findSubTreeSizeRight <- function(node, edgelist, length = 0){
    children <- edgelist[which(edgelist[,1] %in% node),2]
    if(node %in% edgelist[,1]){
        length <- length + 1
        length <- .findSubTreeSize(children[1], edgelist, length)
    }
    return(length)
}

.findSubTreeSize <- function(node, edgelist, length = 0){
    children <- edgelist[which(edgelist[,1] %in% node),2]
    if(node %in% edgelist[,1]){
        length <- length + 1
        left <- .findSubTreeSize(children[1], edgelist, length)
        right <- .findSubTreeSize(children[2], edgelist, length)
        if(left > length || right > length){
            if(left > right){
                return(left)
            } else {
                return(right)
            }
        }
        return(length)
    }
    return(length)
}

.findRoot <- function(edgelist){
    return(unique(edgelist[which( is.na(match(edgelist[,1],
                                              edgelist[,2])) == TRUE)]))
}

.countChildren <- function(node, edgelist, count = -1){
    children <- edgelist[which(edgelist[,1] %in% node),2]
    if(node %in% edgelist[,1]){
        count <- .countChildren(children[1], edgelist, count)
        count <- .countChildren(children[2], edgelist, count)
    }
    return(count+1)
}

.normggSize <- function (gg, mint, maxt) {
    max <- max(igraph::V(gg)$nodeSize)
    min <- min(igraph::V(gg)$nodeSize)
    range1 <- max - min
    intnodes.idx <- !is.na(match(igraph::V(gg)$name, gg$intnodes))
    igraph::V(gg)$nodeSize[!intnodes.idx] <- 
        (igraph::V(gg)$nodeSize[!intnodes.idx] - min)/range1
    igraph::V(gg)$nodeSize[intnodes.idx] <- 1
    range2 <- maxt - mint
    igraph::V(gg)$nodeSize[!intnodes.idx] <- 
        (igraph::V(gg)$nodeSize[!intnodes.idx] * range2) + mint
    return(gg)
}