R/plot_networx.R
In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis
Defines functions
identify.networx
closest.node
closest.edge
plot2D
plotRGL
plot.networx
rotate_matrix
edgeLabels
kugel2kart
kreis2kart
kart2kreis
kart2kugel
coords
coords.equal.angle
spl2angle
circ.mean
deg2rad
rad2deg
Documented in
coords
identify.networx
plot.networx
# some trigonemetric functions
rad2deg <- function(rad) (rad * 180) / (pi)
deg2rad <- function(deg) (deg * pi) / (180)
# circular mean
# https://en.wikipedia.org/wiki/Mean_of_circular_quantities
circ.mean <- function(deg) {
rad.m <- (deg * pi) / (180)
mean.cos <- mean(cos(rad.m))
mean.sin <- mean(sin(rad.m))
theta <- rad2deg(atan(mean.sin / mean.cos))
if (mean.cos < 0) theta <- theta + 180
if ((mean.sin < 0) & (mean.cos > 0)) theta <- theta + 360
theta
}
spl2angle <- function(x) {
l <- length(attr(x, "labels"))
ord <- 1:l
if (!is.null(attr(x, "cycle"))) ord <- attr(x, "cycle")
x <- changeOrder(x, attr(x, "labels")[ord])
y <- lapply(x, function(x, l) (x - 1) / l * 360, l = l)
angle <- vapply(y, circ.mean, 0) |> deg2rad()
# angle <- ((vapply(x, sum, 0) / lengths(x) - 1) / l ) * 2*pi
# kreis2kart(attr(x, "weight"), angle)
angle
}
coords.equal.angle <- function(obj) {
if (is.null(attr(obj, "order")) || (attr(obj, "order") == "postorder"))
obj <- reorder.networx(obj)
spl <- obj$splits
spl <- SHORTwise(spl) #, length(obj$tip.label))
l <- length(obj$edge.length)
# ind1 <- which(!duplicated(obj$splitIndex))
n <- max(obj$edge)
angle <- spl2angle(spl)
weight <- attr(spl, "weight")
k <- matrix(0, max(obj$splitIndex), 2)
res <- matrix(0, max(obj$edge), 2)
for (i in 1:l) { # unique(obj$splitIndex)
j <- obj$edge[i, 1]
m <- obj$edge[i, 2]
p <- obj$splitIndex[i]
res[m, ] <- res[j, ] + kreis2kart(weight[p], angle[p])
}
res
}
#' @rdname phangorn-internal
#' @export
coords <- function(obj, dim = "3D") {
# if(is.null(attr(obj,"order")) || (attr(obj, "order")=="postorder") )
# obj = reorder.networx(obj)
if (dim == "equal_angle") return(coords.equal.angle(obj))
l <- length(obj$edge.length)
ind1 <- which(!duplicated(obj$splitIndex))
n <- max(obj$edge)
adj <- spMatrix(n, n, i = obj$edge[, 2], j = obj$edge[, 1],
x = rep(1, length(obj$edge.length)))
g <- graph_from_adjacency_matrix(adj, "undirected")
if (dim == "3D") {
coord <- layout_nicely(g, dim = 3)
k <- matrix(0, max(obj$splitIndex), 3)
for (i in ind1) {
tmp <- coord[obj$edge[i, 2], ] - coord[obj$edge[i, 1], ]
k[obj$splitIndex[i], ] <- kart2kugel(tmp[1], tmp[2], tmp[3])
}
k[obj$splitIndex[ind1], 1] <- obj$edge.length[ind1]
res <- matrix(0, vcount(g), 3)
for (i in 1:l) {
j <- obj$edge[i, 1]
m <- obj$edge[i, 2]
p <- obj$splitIndex[i]
res[m, ] <- res[j, ] + kugel2kart(k[p, 1], k[p, 2], k[p, 3])
}
}
else {
coord <- layout_nicely(g, dim = 2)
k <- matrix(0, max(obj$splitIndex), 2)
tmp <- coord[obj$edge[ind1, 2], ] - coord[obj$edge[ind1, 1], ]
k[obj$splitIndex[ind1], ] <- kart2kreis(tmp[,1], tmp[,2])
# for (i in ind1) {
# tmp <- coord[obj$edge[i, 2], ] - coord[obj$edge[i, 1], ]
# k[obj$splitIndex[i], ] <- kart2kreis(tmp[1], tmp[2])
# }
k[obj$splitIndex[ind1], 1] <- obj$edge.length[ind1]
res <- matrix(0, vcount(g), 2)
for (i in 1:l) {
j <- obj$edge[i, 1]
m <- obj$edge[i, 2]
p <- obj$splitIndex[i]
res[m, ] <- res[j, ] + kreis2kart(k[p, 1], k[p, 2])
}
}
res
}
kart2kugel <- function(x, y, z) {
r <- sqrt(x * x + y * y + z * z)
alpha <- atan(sqrt(x * x + y * y) / z)
if (z < 0) alpha <- alpha + pi
beta <- atan(y / x)
if (x < 0) beta <- beta + pi
c(r, alpha, beta)
}
kart2kreis <- function(x, y) {
r <- sqrt(x * x + y * y)
alpha <- atan(y / x)
#if (x < 0) alpha <- alpha + pi
if (any(x < 0)) alpha[x < 0] <- alpha[x < 0] + pi
cbind(r, alpha)
}
kreis2kart <- function(r, alpha) {
c(r * cos(alpha), r * sin(alpha))
# if(length(r)>1) return(matrix(c(r*cos(alpha), r*sin(alpha)), ncol=2))
# else return(c(r*cos(alpha), r*sin(alpha)))
}
kugel2kart <- function(r, alpha, beta) {
x <- r * sin(alpha) * cos(beta)
y <- r * sin(alpha) * sin(beta)
z <- r * cos(alpha)
c(x, y, z)
}
edgeLabels <- function(xx, yy, zz = NULL, edge) {
XX <- (xx[edge[, 1]] + xx[edge[, 2]]) / 2
YY <- (yy[edge[, 1]] + yy[edge[, 2]]) / 2
if (!is.null(zz)) {
ZZ <- (zz[edge[, 1]] + zz[edge[, 2]]) / 2
return(cbind(XX, YY, ZZ))
}
cbind(XX, YY)
}
rotate_matrix <- function(x, theta){
rot_matrix <- matrix(c(cos(theta), sin(theta), -sin(theta), cos(theta)),
2, 2, byrow = TRUE)
x %*% rot_matrix
}
#' plot phylogenetic networks
#'
#' So far not all parameters behave the same on the the \code{rgl} \code{"3D"}
#' and basic graphic \code{"2D"} device.
#'
#' Often it is easier and safer to supply vectors of graphical parameters for
#' splits (e.g. splits.color) than for edges. These overwrite values edge.color.
#'
#' @param x an object of class \code{"networx"}
#' @param type "3D" to plot using rgl or "equal angle" and "2D" in the normal
#' device.
#' @param use.edge.length a logical indicating whether to use the edge weights
#' of the network to draw the branches (the default) or not.
#' @param show.tip.label a logical indicating whether to show the tip labels on
#' the graph (defaults to \code{TRUE}, i.e. the labels are shown).
#' @param show.edge.label a logical indicating whether to show the tip labels
#' on the graph.
#' @param edge.label an additional vector of edge labels (normally not needed).
#' @param show.node.label a logical indicating whether to show the node labels
#' (see example).
#' @param node.label an additional vector of node labels (normally not needed).
#' @param show.nodes a logical indicating whether to show the nodes (see
#' example).
#' @param tip.color the colors used for the tip labels.
#' @param edge.color the colors used to draw edges.
#' @param edge.width the width used to draw edges.
#' @param edge.lty a vector of line types.
#' @param split.color the colors used to draw edges.
#' @param split.width the width used to draw edges.
#' @param split.lty a vector of line types.
#' @param font an integer specifying the type of font for the labels: 1 (plain
#' text), 2 (bold), 3 (italic, the default), or 4 (bold italic).
#' @param cex a numeric value giving the factor scaling of the labels.
#' @param cex.node.label a numeric value giving the factor scaling of the node
#' labels.
#' @param cex.edge.label a numeric value giving the factor scaling of the edge
#' labels.
#' @param col.node.label the colors used for the node labels.
#' @param col.edge.label the colors used for the edge labels.
#' @param font.node.label the font used for the node labels.
#' @param font.edge.label the font used for the edge labels.
#' @param underscore a logical specifying whether the underscores in tip labels
#' should be written as spaces (the default) or left as are (if TRUE).
#' @param angle rotate the plot.
#' @param digits if edge labels are numerical a positive integer indicating how
#' many significant digits are to be used.
#' @param \dots Further arguments passed to or from other methods.
#' @returns \code{plot.networx} returns invisibly a list with paramters of the
#' plot.
#' @rdname plot.networx
#' @note The internal representation is likely to change.
#' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
#' @seealso \code{\link{consensusNet}}, \code{\link{neighborNet}},
#' \code{\link{splitsNetwork}}, \code{\link{hadamard}},
#' \code{\link{distanceHadamard}}, \code{\link{as.networx}},
#' \code{\link[ape]{evonet}}, \code{\link[ape]{as.phylo}},
#' \code{\link{densiTree}}, \code{\link[ape]{nodelabels}}
#' @references Dress, A.W.M. and Huson, D.H. (2004) Constructing Splits Graphs
#' \emph{IEEE/ACM Transactions on Computational Biology and Bioinformatics
#' (TCBB)}, \bold{1(3)}, 109--115
#'
#' Schliep, K., Potts, A. J., Morrison, D. A. and Grimm, G. W. (2017),
#' Intertwining phylogenetic trees and networks. \emph{Methods Ecol Evol}.
#' \bold{8}, 1212--1220. doi:10.1111/2041-210X.12760
#' @keywords plot
#' @importFrom igraph make_graph
#' @examples
#'
#' set.seed(1)
#' tree1 <- rtree(20, rooted=FALSE)
#' sp <- as.splits(rNNI(tree1, n=10))
#' net <- as.networx(sp)
#' plot(net)
#' plot(net, direction="axial")
#' \dontrun{
#' # also see example in consensusNet
#' example(consensusNet)
#' }
#' @importFrom igraph graph_from_adjacency_matrix vcount topo_sort layout_nicely
#' @method plot networx
#' @export
plot.networx <- function(x, type = "equal angle", use.edge.length = TRUE,
show.tip.label = TRUE, show.edge.label = FALSE,
edge.label = NULL, show.node.label = FALSE,
node.label = NULL, show.nodes = FALSE,
tip.color = "black", edge.color = "black",
edge.width = 3, edge.lty = 1, split.color = NULL,
split.width = NULL, split.lty = NULL, font = 3,
cex = par("cex"), cex.node.label = cex,
cex.edge.label = cex, col.node.label = tip.color,
col.edge.label = tip.color, font.node.label = font,
font.edge.label = font, underscore = FALSE,
angle=0, digits=3, ...) {
type <- match.arg(type, c("equal angle", "3D", "2D"))
if (use.edge.length == FALSE){
x$edge.length[] <- 1
attr(x$splits, "weight") <- rep(1, length(x$splits))
}
nTips <- length(x$tip.label)
conf <- attr(x$splits, "confidences")
index <- x$splitIndex
if(!is.null(edge.label) && is.numeric(edge.label)) edge.label <- prettyNum(edge.label)
if (is.null(edge.label) && !is.null(conf)) {
conf <- conf[index]
if(is.numeric(conf)) conf <- prettyNum(format(conf, digits=digits))
if (!is.null(x$translate)) conf[match(x$translate$node, x$edge[, 2])] <- ""
else conf[x$edge[, 2] <= nTips] <- ""
edge.label <- conf
}
if (is.null(node.label)) node.label <- as.character(1:max(x$edge))
if (show.tip.label) node.label[1:nTips] <- ""
if (show.tip.label){
if (is.expression(x$tip.label)) underscore <- TRUE
if (!underscore) x$tip.label <- gsub("_", " ", x$tip.label)
}
lspl <- max(x$splitIndex)
if (!is.null(split.color)) {
if (length(split.color) != lspl)
stop("split.color must be same length as splits")
else edge.color <- split.color[x$splitIndex]
}
if (!is.null(split.width)) {
if (length(split.width) != lspl)
stop("split.color must be same length as splits")
else edge.width <- split.width[x$splitIndex]
}
if (!is.null(split.lty)) {
if (length(split.lty) != lspl)
stop("split.color must be same length as splits")
else edge.lty <- split.lty[x$splitIndex]
}
chk <- FALSE
if (type == "3D") chk <- requireNamespace("rgl", quietly = TRUE)
if (!chk && type == "3D") {
warning("type='3D' requires the package 'rgl', plotting in '2D' instead!\n")
type <- "2D"
}
# use precomputed vertices when available
coord <- NULL
if (!is.null(x$.plot)) coord <- x$.plot$vertices
if (type == "3D") {
if (is.null(coord) || ncol(coord) != 3)
coord <- coords(x, dim = "3D")
plotRGL(coord, x, show.tip.label = show.tip.label,
show.edge.label = show.edge.label, edge.label = edge.label,
show.node.label = show.node.label, node.label = node.label,
show.nodes = show.nodes, tip.color = tip.color, edge.color = edge.color,
edge.width = edge.width, font = font, cex = cex,
cex.node.label = cex.node.label, cex.edge.label = cex.edge.label,
col.node.label = col.node.label, col.edge.label = col.edge.label,
font.node.label = font.node.label, font.edge.label = font.edge.label)
}
else {
if (is.null(coord) || ncol(coord) != 2) {
if (type == "equal angle") coord <- coords.equal.angle(x)
else coord <- coords(x, dim = "2D")
}
if(angle != 0){
angle <- angle * pi/180 #
coord <- rotate_matrix(coord, angle)
}
plot2D(coord, x, show.tip.label = show.tip.label,
show.edge.label = show.edge.label, edge.label = edge.label,
show.node.label = show.node.label, node.label = node.label,
show.nodes = show.nodes, tip.color = tip.color, edge.color = edge.color,
edge.width = edge.width, edge.lty = edge.lty, font = font, cex = cex,
cex.node.label = cex.node.label, cex.edge.label = cex.edge.label,
col.node.label = col.node.label, col.edge.label = col.edge.label,
font.node.label = font.node.label, font.edge.label = font.edge.label,
add = FALSE, ...)
}
x$.plot <- list(vertices = coord, edge.color = edge.color,
edge.width = edge.width, edge.lty = edge.lty)
invisible(x)
}
plotRGL <- function(coords, net, show.tip.label = TRUE, show.edge.label = FALSE,
edge.label = NULL, show.node.label = FALSE,
node.label = NULL, show.nodes = FALSE, tip.color = "blue",
edge.color = "grey", edge.width = 3, font = 3,
cex = par("cex"), cex.node.label = cex,
cex.edge.label = cex, col.node.label = tip.color,
col.edge.label = tip.color, font.node.label = font,
font.edge.label = font, ...) {
open3d <- rgl::open3d
segments3d <- rgl::segments3d
spheres3d <- rgl::spheres3d
texts3d <- rgl::texts3d
edge <- net$edge
x <- coords[, 1]
y <- coords[, 2]
z <- coords[, 3]
nTips <- length(net$tip.label)
segments3d(x[t(edge)], y[t(edge)], z[t(edge)],
col = rep(edge.color, each = 2), lwd = edge.width)
radius <- 0
if (show.nodes) {
radius <- sqrt( (max(x) - min(x))^2 + (max(y) - min(y))^2 +
(max(z) - min(z))^2) / 200
spheres3d(x[1:nTips], y[1:nTips], z[1:nTips], radius = 2 * radius,
color = "cyan")
spheres3d(x[-c(1:nTips)], y[-c(1:nTips)], z[-c(1:nTips)], radius = radius,
color = "magenta")
}
if (show.tip.label) {
if (is.null(net$translate))
texts3d(x[1:nTips] + 2.05 * radius, y[1:nTips], z[1:nTips],
net$tip.label, color = tip.color, cex = cex, font = font)
else
texts3d(x[net$translate$node] + 2.05 * radius, y[net$translate$node],
z[net$translate$node], net$tip.label, color = tip.color, cex = cex,
font = font)
}
if (show.edge.label) {
ec <- edgeLabels(x, y, z, edge)
if (is.null(edge.label)) edge.label <- net$splitIndex
# else edge.label = net$splitIndex
texts3d(ec[, 1], ec[, 2], ec[, 3], edge.label, color = col.edge.label,
cex = cex.edge.label, font = font.edge.label)
}
if (show.node.label) {
texts3d(x, y, z, node.label, color = col.node.label, cex = cex.node.label,
font = font.node.label)
}
}
plot2D <- function(coords, net, show.tip.label = TRUE, show.edge.label = FALSE,
edge.label = NULL, show.node.label = FALSE,
node.label = NULL, tip.color = "blue", edge.color = "grey",
edge.width = 3, edge.lty = 1, font = 3, cex = par("cex"),
cex.node.label = cex, cex.edge.label = cex,
col.node.label = tip.color, col.edge.label = tip.color,
font.node.label = font, font.edge.label = font,
add = FALSE, direction="horizontal", xlim=NULL, ylim=NULL,
...) {
direction <- match.arg(direction, c("horizontal", "axial"))
edge <- net$edge
label <- net$tip.label
xx <- coords[, 1]
yy <- coords[, 2]
nTips <- length(label)
if(is.null(xlim)){
xlim <- range(xx)
offset <- max(nchar(label)) * 0.018 * cex * diff(xlim)
if (show.tip.label) xlim <- c(xlim[1] - offset, xlim[2] + offset)
}
if(is.null(ylim)){
ylim <- range(yy)
if (show.tip.label){
if(direction=="axial"){
offset <- max(nchar(label)) * 0.018 * cex * diff(ylim)
ylim <- c(ylim[1] - offset, ylim[2] + offset)
} else ylim <- c(ylim[1] - 0.03 * cex * diff(ylim),
ylim[2] + 0.03 * cex * diff(ylim))
}
}
if (!add) {
plot.new()
plot.window(xlim, ylim, asp = 1)
}
cladogram.plot(edge, xx, yy, edge.color, edge.width, edge.lty)
if (show.tip.label) {
if (is.null(net$translate)) ind <- match(1:nTips, edge[, 2])
else ind <- match(net$translate$node, edge[, 2])
if(direction=="horizontal"){
pos <- rep(4, nTips)
XX <- xx[edge[ind, 1]] - xx[edge[ind, 2]]
pos[XX > 0] <- 2
YY <- yy[edge[ind, 1]] - yy[edge[ind, 2]]
pos2 <- rep(3, nTips)
pos2[YY > 0] <- 1
# needed if tiplabels are not at internal nodes
XX[is.na(XX)] <- 0
YY[is.na(YY)] <- 0
pos[abs(YY) > abs(XX)] <- pos2[abs(YY) > abs(XX)]
if (is.null(net$translate)) text(xx[1:nTips], yy[1:nTips], labels = label,
pos = pos, col = tip.color, cex = cex, font = font)
else text(xx[net$translate$node], yy[net$translate$node], labels = label,
pos = pos, col = tip.color, cex = cex, font = font)
}
else {
XX <- xx[edge[ind, 2]] - xx[edge[ind, 1]]
YY <- yy[edge[ind, 2]] - yy[edge[ind, 1]]
angle <- kart2kreis(XX, YY)[,2]
adj <- abs(angle) > pi/2
angle <- angle * 180/pi # switch to degrees
angle[adj] <- angle[adj] - 180
adj <- as.numeric(adj)
## `srt' takes only a single value, so can't vectorize this:
## (and need to 'elongate' these vectors:)
font <- rep(font, length.out = nTips)
tip.color <- rep(tip.color, length.out = nTips)
cex <- rep(cex, length.out = nTips)
for (i in seq_along(label))
text(xx[i], yy[i], label[i], font = font[i],
cex = cex[i], srt = angle[i], adj = adj[i],
col = tip.color[i])
}
}
if (show.edge.label) {
ec <- edgeLabels(xx, yy, edge = edge)
if (is.null(edge.label)) edge.label <- net$splitIndex
# show only one edge label
em <- apply(ec, 1, function(x) max(abs(x)))
si <- net$splitIndex
for (i in unique(si)) {
tmp <- si == i
if (sum(tmp) > 1) {
w <- which(tmp)
wm <- which.max(em[w])
edge.label[w[-wm]] <- ""
}
}
text(ec[, 1], ec[, 2], labels = edge.label, col = col.edge.label,
cex = cex.edge.label, font = font.edge.label)
}
if (show.node.label) {
text(xx, yy, labels = node.label, col = col.node.label,
cex = cex.node.label, font = font.node.label)
}
PP <- list(Ntip = nTips, type = "networx", edge = net$edge, xx = coords[, 1],
yy = coords[, 2], x.lim=xlim, y.lim=ylim, align.tip.label=FALSE)
assign("last_plot.phylo", PP, envir = .PlotPhyloEnv)
}
closest.edge <- function(x, y, P1, P2) {
x1 <- P1[, 1]
x2 <- P2[, 1]
y1 <- P1[, 2]
y2 <- P2[, 2]
A <- sqrt( (x2 - x)^2 + (y2 - y)^2) # d_BC
B <- sqrt( (x1 - x)^2 + (y1 - y)^2) # d_AC
C <- sqrt( (x1 - x2)^2 + (y1 - y2)^2) # d_AB
# Kosinussatz
alpha <- acos( (B^2 + C^2 - A^2) / (2 * B * C))
beta <- acos( (A^2 + C^2 - B^2) / (2 * A * C))
d <- abs( (y2 - y1) * x - (x2 - x1) * y + x2 * y1 - y2 * x1) /
sqrt( (y2 - y1)^2 + (x2 - x1)^2)
d[alpha > (pi / 2)] <- B[alpha > (pi / 2)]
d[beta > (pi / 2)] <- A[beta > (pi / 2)]
d
}
closest.node <- function(x, y, P) {
x1 <- P[, 1]
y1 <- P[, 2]
d <- sqrt((x1 - x)^2 + (y1 - y)^2)
d
}
#' Identify splits in a network
#'
#' \code{identify.networx} reads the position of the graphics pointer when the
#' mouse button is pressed. It then returns the split belonging to the edge
#' closest to the pointer. The network must be plotted beforehand.
#'
#' @param x an object of class \code{networx}
#' @param quiet a logical controlling whether to print a message inviting the
#' user to click on the tree.
#' @param \dots further arguments to be passed to or from other methods.
#' @return \code{identify.networx} returns a splits object.
#' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
#' @seealso \code{\link[phangorn]{plot.networx}},
#' \code{\link[graphics]{identify}}
#' @examples
#' \dontrun{
#' data(yeast)
#' dm <- dist.ml(yeast)
#' nnet <- neighborNet(dm)
#' plot(nnet)
#' identify(nnet) # click close to an edge
#' }
#' @importFrom graphics identify
#' @method identify networx
#' @export
identify.networx <- function(x, quiet = FALSE, ...) {
if (!quiet)
cat("Click close to a node or edge of the tree...\n")
xy <- locator(1)
if (is.null(xy))
return(NULL)
if (is.null(x$.plot)) {
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
edge <- lastPP$edge
xx <- lastPP$xx
yy <- lastPP$yy
vertices <- cbind(xx, yy)
}
else {
lastPP <- x$.plot
edge <- x$edge
vertices <- lastPP$vertices
}
P1 <- vertices[edge[, 1], , drop = FALSE]
P2 <- vertices[edge[, 2], , drop = FALSE]
d <- closest.edge(xy$x, xy$y, P1, P2)
split <- x$splitIndex[which.min(d)]
x$splits[split]
}
KlausVigo/phangorn documentation built on June 23, 2024, 10:49 p.m.
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Defines functions identify.networx closest.node closest.edge plot2D plotRGL plot.networx rotate_matrix edgeLabels kugel2kart kreis2kart kart2kreis kart2kugel coords coords.equal.angle spl2angle circ.mean deg2rad rad2deg
Documented in coords identify.networx plot.networx
# some trigonemetric functions
rad2deg <- function(rad) (rad * 180) / (pi)
deg2rad <- function(deg) (deg * pi) / (180)
# circular mean
# https://en.wikipedia.org/wiki/Mean_of_circular_quantities
circ.mean <- function(deg) {
rad.m <- (deg * pi) / (180)
mean.cos <- mean(cos(rad.m))
mean.sin <- mean(sin(rad.m))
theta <- rad2deg(atan(mean.sin / mean.cos))
if (mean.cos < 0) theta <- theta + 180
if ((mean.sin < 0) & (mean.cos > 0)) theta <- theta + 360
theta
}
spl2angle <- function(x) {
l <- length(attr(x, "labels"))
ord <- 1:l
if (!is.null(attr(x, "cycle"))) ord <- attr(x, "cycle")
x <- changeOrder(x, attr(x, "labels")[ord])
y <- lapply(x, function(x, l) (x - 1) / l * 360, l = l)
angle <- vapply(y, circ.mean, 0) |> deg2rad()
# angle <- ((vapply(x, sum, 0) / lengths(x) - 1) / l ) * 2*pi
# kreis2kart(attr(x, "weight"), angle)
angle
}
coords.equal.angle <- function(obj) {
if (is.null(attr(obj, "order")) || (attr(obj, "order") == "postorder"))
obj <- reorder.networx(obj)
spl <- obj$splits
spl <- SHORTwise(spl) #, length(obj$tip.label))
l <- length(obj$edge.length)
# ind1 <- which(!duplicated(obj$splitIndex))
n <- max(obj$edge)
angle <- spl2angle(spl)
weight <- attr(spl, "weight")
k <- matrix(0, max(obj$splitIndex), 2)
res <- matrix(0, max(obj$edge), 2)
for (i in 1:l) { # unique(obj$splitIndex)
j <- obj$edge[i, 1]
m <- obj$edge[i, 2]
p <- obj$splitIndex[i]
res[m, ] <- res[j, ] + kreis2kart(weight[p], angle[p])
}
res
}
#' @rdname phangorn-internal
#' @export
coords <- function(obj, dim = "3D") {
# if(is.null(attr(obj,"order")) || (attr(obj, "order")=="postorder") )
# obj = reorder.networx(obj)
if (dim == "equal_angle") return(coords.equal.angle(obj))
l <- length(obj$edge.length)
ind1 <- which(!duplicated(obj$splitIndex))
n <- max(obj$edge)
adj <- spMatrix(n, n, i = obj$edge[, 2], j = obj$edge[, 1],
x = rep(1, length(obj$edge.length)))
g <- graph_from_adjacency_matrix(adj, "undirected")
if (dim == "3D") {
coord <- layout_nicely(g, dim = 3)
k <- matrix(0, max(obj$splitIndex), 3)
for (i in ind1) {
tmp <- coord[obj$edge[i, 2], ] - coord[obj$edge[i, 1], ]
k[obj$splitIndex[i], ] <- kart2kugel(tmp[1], tmp[2], tmp[3])
}
k[obj$splitIndex[ind1], 1] <- obj$edge.length[ind1]
res <- matrix(0, vcount(g), 3)
for (i in 1:l) {
j <- obj$edge[i, 1]
m <- obj$edge[i, 2]
p <- obj$splitIndex[i]
res[m, ] <- res[j, ] + kugel2kart(k[p, 1], k[p, 2], k[p, 3])
}
}
else {
coord <- layout_nicely(g, dim = 2)
k <- matrix(0, max(obj$splitIndex), 2)
tmp <- coord[obj$edge[ind1, 2], ] - coord[obj$edge[ind1, 1], ]
k[obj$splitIndex[ind1], ] <- kart2kreis(tmp[,1], tmp[,2])
# for (i in ind1) {
# tmp <- coord[obj$edge[i, 2], ] - coord[obj$edge[i, 1], ]
# k[obj$splitIndex[i], ] <- kart2kreis(tmp[1], tmp[2])
# }
k[obj$splitIndex[ind1], 1] <- obj$edge.length[ind1]
res <- matrix(0, vcount(g), 2)
for (i in 1:l) {
j <- obj$edge[i, 1]
m <- obj$edge[i, 2]
p <- obj$splitIndex[i]
res[m, ] <- res[j, ] + kreis2kart(k[p, 1], k[p, 2])
}
}
res
}
kart2kugel <- function(x, y, z) {
r <- sqrt(x * x + y * y + z * z)
alpha <- atan(sqrt(x * x + y * y) / z)
if (z < 0) alpha <- alpha + pi
beta <- atan(y / x)
if (x < 0) beta <- beta + pi
c(r, alpha, beta)
}
kart2kreis <- function(x, y) {
r <- sqrt(x * x + y * y)
alpha <- atan(y / x)
#if (x < 0) alpha <- alpha + pi
if (any(x < 0)) alpha[x < 0] <- alpha[x < 0] + pi
cbind(r, alpha)
}
kreis2kart <- function(r, alpha) {
c(r * cos(alpha), r * sin(alpha))
# if(length(r)>1) return(matrix(c(r*cos(alpha), r*sin(alpha)), ncol=2))
# else return(c(r*cos(alpha), r*sin(alpha)))
}
kugel2kart <- function(r, alpha, beta) {
x <- r * sin(alpha) * cos(beta)
y <- r * sin(alpha) * sin(beta)
z <- r * cos(alpha)
c(x, y, z)
}
edgeLabels <- function(xx, yy, zz = NULL, edge) {
XX <- (xx[edge[, 1]] + xx[edge[, 2]]) / 2
YY <- (yy[edge[, 1]] + yy[edge[, 2]]) / 2
if (!is.null(zz)) {
ZZ <- (zz[edge[, 1]] + zz[edge[, 2]]) / 2
return(cbind(XX, YY, ZZ))
}
cbind(XX, YY)
}
rotate_matrix <- function(x, theta){
rot_matrix <- matrix(c(cos(theta), sin(theta), -sin(theta), cos(theta)),
2, 2, byrow = TRUE)
x %*% rot_matrix
}
#' plot phylogenetic networks
#'
#' So far not all parameters behave the same on the the \code{rgl} \code{"3D"}
#' and basic graphic \code{"2D"} device.
#'
#' Often it is easier and safer to supply vectors of graphical parameters for
#' splits (e.g. splits.color) than for edges. These overwrite values edge.color.
#'
#' @param x an object of class \code{"networx"}
#' @param type "3D" to plot using rgl or "equal angle" and "2D" in the normal
#' device.
#' @param use.edge.length a logical indicating whether to use the edge weights
#' of the network to draw the branches (the default) or not.
#' @param show.tip.label a logical indicating whether to show the tip labels on
#' the graph (defaults to \code{TRUE}, i.e. the labels are shown).
#' @param show.edge.label a logical indicating whether to show the tip labels
#' on the graph.
#' @param edge.label an additional vector of edge labels (normally not needed).
#' @param show.node.label a logical indicating whether to show the node labels
#' (see example).
#' @param node.label an additional vector of node labels (normally not needed).
#' @param show.nodes a logical indicating whether to show the nodes (see
#' example).
#' @param tip.color the colors used for the tip labels.
#' @param edge.color the colors used to draw edges.
#' @param edge.width the width used to draw edges.
#' @param edge.lty a vector of line types.
#' @param split.color the colors used to draw edges.
#' @param split.width the width used to draw edges.
#' @param split.lty a vector of line types.
#' @param font an integer specifying the type of font for the labels: 1 (plain
#' text), 2 (bold), 3 (italic, the default), or 4 (bold italic).
#' @param cex a numeric value giving the factor scaling of the labels.
#' @param cex.node.label a numeric value giving the factor scaling of the node
#' labels.
#' @param cex.edge.label a numeric value giving the factor scaling of the edge
#' labels.
#' @param col.node.label the colors used for the node labels.
#' @param col.edge.label the colors used for the edge labels.
#' @param font.node.label the font used for the node labels.
#' @param font.edge.label the font used for the edge labels.
#' @param underscore a logical specifying whether the underscores in tip labels
#' should be written as spaces (the default) or left as are (if TRUE).
#' @param angle rotate the plot.
#' @param digits if edge labels are numerical a positive integer indicating how
#' many significant digits are to be used.
#' @param \dots Further arguments passed to or from other methods.
#' @returns \code{plot.networx} returns invisibly a list with paramters of the
#' plot.
#' @rdname plot.networx
#' @note The internal representation is likely to change.
#' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
#' @seealso \code{\link{consensusNet}}, \code{\link{neighborNet}},
#' \code{\link{splitsNetwork}}, \code{\link{hadamard}},
#' \code{\link{distanceHadamard}}, \code{\link{as.networx}},
#' \code{\link[ape]{evonet}}, \code{\link[ape]{as.phylo}},
#' \code{\link{densiTree}}, \code{\link[ape]{nodelabels}}
#' @references Dress, A.W.M. and Huson, D.H. (2004) Constructing Splits Graphs
#' \emph{IEEE/ACM Transactions on Computational Biology and Bioinformatics
#' (TCBB)}, \bold{1(3)}, 109--115
#'
#' Schliep, K., Potts, A. J., Morrison, D. A. and Grimm, G. W. (2017),
#' Intertwining phylogenetic trees and networks. \emph{Methods Ecol Evol}.
#' \bold{8}, 1212--1220. doi:10.1111/2041-210X.12760
#' @keywords plot
#' @importFrom igraph make_graph
#' @examples
#'
#' set.seed(1)
#' tree1 <- rtree(20, rooted=FALSE)
#' sp <- as.splits(rNNI(tree1, n=10))
#' net <- as.networx(sp)
#' plot(net)
#' plot(net, direction="axial")
#' \dontrun{
#' # also see example in consensusNet
#' example(consensusNet)
#' }
#' @importFrom igraph graph_from_adjacency_matrix vcount topo_sort layout_nicely
#' @method plot networx
#' @export
plot.networx <- function(x, type = "equal angle", use.edge.length = TRUE,
show.tip.label = TRUE, show.edge.label = FALSE,
edge.label = NULL, show.node.label = FALSE,
node.label = NULL, show.nodes = FALSE,
tip.color = "black", edge.color = "black",
edge.width = 3, edge.lty = 1, split.color = NULL,
split.width = NULL, split.lty = NULL, font = 3,
cex = par("cex"), cex.node.label = cex,
cex.edge.label = cex, col.node.label = tip.color,
col.edge.label = tip.color, font.node.label = font,
font.edge.label = font, underscore = FALSE,
angle=0, digits=3, ...) {
type <- match.arg(type, c("equal angle", "3D", "2D"))
if (use.edge.length == FALSE){
x$edge.length[] <- 1
attr(x$splits, "weight") <- rep(1, length(x$splits))
}
nTips <- length(x$tip.label)
conf <- attr(x$splits, "confidences")
index <- x$splitIndex
if(!is.null(edge.label) && is.numeric(edge.label)) edge.label <- prettyNum(edge.label)
if (is.null(edge.label) && !is.null(conf)) {
conf <- conf[index]
if(is.numeric(conf)) conf <- prettyNum(format(conf, digits=digits))
if (!is.null(x$translate)) conf[match(x$translate$node, x$edge[, 2])] <- ""
else conf[x$edge[, 2] <= nTips] <- ""
edge.label <- conf
}
if (is.null(node.label)) node.label <- as.character(1:max(x$edge))
if (show.tip.label) node.label[1:nTips] <- ""
if (show.tip.label){
if (is.expression(x$tip.label)) underscore <- TRUE
if (!underscore) x$tip.label <- gsub("_", " ", x$tip.label)
}
lspl <- max(x$splitIndex)
if (!is.null(split.color)) {
if (length(split.color) != lspl)
stop("split.color must be same length as splits")
else edge.color <- split.color[x$splitIndex]
}
if (!is.null(split.width)) {
if (length(split.width) != lspl)
stop("split.color must be same length as splits")
else edge.width <- split.width[x$splitIndex]
}
if (!is.null(split.lty)) {
if (length(split.lty) != lspl)
stop("split.color must be same length as splits")
else edge.lty <- split.lty[x$splitIndex]
}
chk <- FALSE
if (type == "3D") chk <- requireNamespace("rgl", quietly = TRUE)
if (!chk && type == "3D") {
warning("type='3D' requires the package 'rgl', plotting in '2D' instead!\n")
type <- "2D"
}
# use precomputed vertices when available
coord <- NULL
if (!is.null(x$.plot)) coord <- x$.plot$vertices
if (type == "3D") {
if (is.null(coord) || ncol(coord) != 3)
coord <- coords(x, dim = "3D")
plotRGL(coord, x, show.tip.label = show.tip.label,
show.edge.label = show.edge.label, edge.label = edge.label,
show.node.label = show.node.label, node.label = node.label,
show.nodes = show.nodes, tip.color = tip.color, edge.color = edge.color,
edge.width = edge.width, font = font, cex = cex,
cex.node.label = cex.node.label, cex.edge.label = cex.edge.label,
col.node.label = col.node.label, col.edge.label = col.edge.label,
font.node.label = font.node.label, font.edge.label = font.edge.label)
}
else {
if (is.null(coord) || ncol(coord) != 2) {
if (type == "equal angle") coord <- coords.equal.angle(x)
else coord <- coords(x, dim = "2D")
}
if(angle != 0){
angle <- angle * pi/180 #
coord <- rotate_matrix(coord, angle)
}
plot2D(coord, x, show.tip.label = show.tip.label,
show.edge.label = show.edge.label, edge.label = edge.label,
show.node.label = show.node.label, node.label = node.label,
show.nodes = show.nodes, tip.color = tip.color, edge.color = edge.color,
edge.width = edge.width, edge.lty = edge.lty, font = font, cex = cex,
cex.node.label = cex.node.label, cex.edge.label = cex.edge.label,
col.node.label = col.node.label, col.edge.label = col.edge.label,
font.node.label = font.node.label, font.edge.label = font.edge.label,
add = FALSE, ...)
}
x$.plot <- list(vertices = coord, edge.color = edge.color,
edge.width = edge.width, edge.lty = edge.lty)
invisible(x)
}
plotRGL <- function(coords, net, show.tip.label = TRUE, show.edge.label = FALSE,
edge.label = NULL, show.node.label = FALSE,
node.label = NULL, show.nodes = FALSE, tip.color = "blue",
edge.color = "grey", edge.width = 3, font = 3,
cex = par("cex"), cex.node.label = cex,
cex.edge.label = cex, col.node.label = tip.color,
col.edge.label = tip.color, font.node.label = font,
font.edge.label = font, ...) {
open3d <- rgl::open3d
segments3d <- rgl::segments3d
spheres3d <- rgl::spheres3d
texts3d <- rgl::texts3d
edge <- net$edge
x <- coords[, 1]
y <- coords[, 2]
z <- coords[, 3]
nTips <- length(net$tip.label)
segments3d(x[t(edge)], y[t(edge)], z[t(edge)],
col = rep(edge.color, each = 2), lwd = edge.width)
radius <- 0
if (show.nodes) {
radius <- sqrt( (max(x) - min(x))^2 + (max(y) - min(y))^2 +
(max(z) - min(z))^2) / 200
spheres3d(x[1:nTips], y[1:nTips], z[1:nTips], radius = 2 * radius,
color = "cyan")
spheres3d(x[-c(1:nTips)], y[-c(1:nTips)], z[-c(1:nTips)], radius = radius,
color = "magenta")
}
if (show.tip.label) {
if (is.null(net$translate))
texts3d(x[1:nTips] + 2.05 * radius, y[1:nTips], z[1:nTips],
net$tip.label, color = tip.color, cex = cex, font = font)
else
texts3d(x[net$translate$node] + 2.05 * radius, y[net$translate$node],
z[net$translate$node], net$tip.label, color = tip.color, cex = cex,
font = font)
}
if (show.edge.label) {
ec <- edgeLabels(x, y, z, edge)
if (is.null(edge.label)) edge.label <- net$splitIndex
# else edge.label = net$splitIndex
texts3d(ec[, 1], ec[, 2], ec[, 3], edge.label, color = col.edge.label,
cex = cex.edge.label, font = font.edge.label)
}
if (show.node.label) {
texts3d(x, y, z, node.label, color = col.node.label, cex = cex.node.label,
font = font.node.label)
}
}
plot2D <- function(coords, net, show.tip.label = TRUE, show.edge.label = FALSE,
edge.label = NULL, show.node.label = FALSE,
node.label = NULL, tip.color = "blue", edge.color = "grey",
edge.width = 3, edge.lty = 1, font = 3, cex = par("cex"),
cex.node.label = cex, cex.edge.label = cex,
col.node.label = tip.color, col.edge.label = tip.color,
font.node.label = font, font.edge.label = font,
add = FALSE, direction="horizontal", xlim=NULL, ylim=NULL,
...) {
direction <- match.arg(direction, c("horizontal", "axial"))
edge <- net$edge
label <- net$tip.label
xx <- coords[, 1]
yy <- coords[, 2]
nTips <- length(label)
if(is.null(xlim)){
xlim <- range(xx)
offset <- max(nchar(label)) * 0.018 * cex * diff(xlim)
if (show.tip.label) xlim <- c(xlim[1] - offset, xlim[2] + offset)
}
if(is.null(ylim)){
ylim <- range(yy)
if (show.tip.label){
if(direction=="axial"){
offset <- max(nchar(label)) * 0.018 * cex * diff(ylim)
ylim <- c(ylim[1] - offset, ylim[2] + offset)
} else ylim <- c(ylim[1] - 0.03 * cex * diff(ylim),
ylim[2] + 0.03 * cex * diff(ylim))
}
}
if (!add) {
plot.new()
plot.window(xlim, ylim, asp = 1)
}
cladogram.plot(edge, xx, yy, edge.color, edge.width, edge.lty)
if (show.tip.label) {
if (is.null(net$translate)) ind <- match(1:nTips, edge[, 2])
else ind <- match(net$translate$node, edge[, 2])
if(direction=="horizontal"){
pos <- rep(4, nTips)
XX <- xx[edge[ind, 1]] - xx[edge[ind, 2]]
pos[XX > 0] <- 2
YY <- yy[edge[ind, 1]] - yy[edge[ind, 2]]
pos2 <- rep(3, nTips)
pos2[YY > 0] <- 1
# needed if tiplabels are not at internal nodes
XX[is.na(XX)] <- 0
YY[is.na(YY)] <- 0
pos[abs(YY) > abs(XX)] <- pos2[abs(YY) > abs(XX)]
if (is.null(net$translate)) text(xx[1:nTips], yy[1:nTips], labels = label,
pos = pos, col = tip.color, cex = cex, font = font)
else text(xx[net$translate$node], yy[net$translate$node], labels = label,
pos = pos, col = tip.color, cex = cex, font = font)
}
else {
XX <- xx[edge[ind, 2]] - xx[edge[ind, 1]]
YY <- yy[edge[ind, 2]] - yy[edge[ind, 1]]
angle <- kart2kreis(XX, YY)[,2]
adj <- abs(angle) > pi/2
angle <- angle * 180/pi # switch to degrees
angle[adj] <- angle[adj] - 180
adj <- as.numeric(adj)
## `srt' takes only a single value, so can't vectorize this:
## (and need to 'elongate' these vectors:)
font <- rep(font, length.out = nTips)
tip.color <- rep(tip.color, length.out = nTips)
cex <- rep(cex, length.out = nTips)
for (i in seq_along(label))
text(xx[i], yy[i], label[i], font = font[i],
cex = cex[i], srt = angle[i], adj = adj[i],
col = tip.color[i])
}
}
if (show.edge.label) {
ec <- edgeLabels(xx, yy, edge = edge)
if (is.null(edge.label)) edge.label <- net$splitIndex
# show only one edge label
em <- apply(ec, 1, function(x) max(abs(x)))
si <- net$splitIndex
for (i in unique(si)) {
tmp <- si == i
if (sum(tmp) > 1) {
w <- which(tmp)
wm <- which.max(em[w])
edge.label[w[-wm]] <- ""
}
}
text(ec[, 1], ec[, 2], labels = edge.label, col = col.edge.label,
cex = cex.edge.label, font = font.edge.label)
}
if (show.node.label) {
text(xx, yy, labels = node.label, col = col.node.label,
cex = cex.node.label, font = font.node.label)
}
PP <- list(Ntip = nTips, type = "networx", edge = net$edge, xx = coords[, 1],
yy = coords[, 2], x.lim=xlim, y.lim=ylim, align.tip.label=FALSE)
assign("last_plot.phylo", PP, envir = .PlotPhyloEnv)
}
closest.edge <- function(x, y, P1, P2) {
x1 <- P1[, 1]
x2 <- P2[, 1]
y1 <- P1[, 2]
y2 <- P2[, 2]
A <- sqrt( (x2 - x)^2 + (y2 - y)^2) # d_BC
B <- sqrt( (x1 - x)^2 + (y1 - y)^2) # d_AC
C <- sqrt( (x1 - x2)^2 + (y1 - y2)^2) # d_AB
# Kosinussatz
alpha <- acos( (B^2 + C^2 - A^2) / (2 * B * C))
beta <- acos( (A^2 + C^2 - B^2) / (2 * A * C))
d <- abs( (y2 - y1) * x - (x2 - x1) * y + x2 * y1 - y2 * x1) /
sqrt( (y2 - y1)^2 + (x2 - x1)^2)
d[alpha > (pi / 2)] <- B[alpha > (pi / 2)]
d[beta > (pi / 2)] <- A[beta > (pi / 2)]
d
}
closest.node <- function(x, y, P) {
x1 <- P[, 1]
y1 <- P[, 2]
d <- sqrt((x1 - x)^2 + (y1 - y)^2)
d
}
#' Identify splits in a network
#'
#' \code{identify.networx} reads the position of the graphics pointer when the
#' mouse button is pressed. It then returns the split belonging to the edge
#' closest to the pointer. The network must be plotted beforehand.
#'
#' @param x an object of class \code{networx}
#' @param quiet a logical controlling whether to print a message inviting the
#' user to click on the tree.
#' @param \dots further arguments to be passed to or from other methods.
#' @return \code{identify.networx} returns a splits object.
#' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
#' @seealso \code{\link[phangorn]{plot.networx}},
#' \code{\link[graphics]{identify}}
#' @examples
#' \dontrun{
#' data(yeast)
#' dm <- dist.ml(yeast)
#' nnet <- neighborNet(dm)
#' plot(nnet)
#' identify(nnet) # click close to an edge
#' }
#' @importFrom graphics identify
#' @method identify networx
#' @export
identify.networx <- function(x, quiet = FALSE, ...) {
if (!quiet)
cat("Click close to a node or edge of the tree...\n")
xy <- locator(1)
if (is.null(xy))
return(NULL)
if (is.null(x$.plot)) {
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
edge <- lastPP$edge
xx <- lastPP$xx
yy <- lastPP$yy
vertices <- cbind(xx, yy)
}
else {
lastPP <- x$.plot
edge <- x$edge
vertices <- lastPP$vertices
}
P1 <- vertices[edge[, 1], , drop = FALSE]
P2 <- vertices[edge[, 2], , drop = FALSE]
d <- closest.edge(xy$x, xy$y, P1, P2)
split <- x$splitIndex[which.min(d)]
x$splits[split]
}
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