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# Copyright (C) Tal Galili
#
# This file is part of dendextend.
#
# dendextend is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# dendextend is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
#
### An internal function for plot_horiz.dendrogram
### This is basically "plotNode", but with options to make it work
### with horizontal trees.
plotNode_horiz <- function(x1, x2, subtree, type, center, leaflab, dLeaf, nodePar,
edgePar, horiz = FALSE,
text_pos = 2, text_offset = 0) {
.midDend <- stats_.midDend
plotNodeLimit <- stats_plotNodeLimit
plotNode <- stats_plotNode
inner <- !is.leaf(subtree) && x1 != x2
yTop <- attr(subtree, "height")
bx <- plotNodeLimit(x1, x2, subtree, center)
xTop <- bx$x
hasP <- !is.null(nPar <- attr(subtree, "nodePar"))
if (!hasP) {
nPar <- nodePar
}
if (getOption("verbose")) {
cat(if (inner) {
"inner node"
} else {
"leaf"
}, ":")
if (!is.null(nPar)) {
cat(" with node pars\n")
str(nPar)
}
cat(if (inner) {
paste(" height", formatC(yTop), "; ")
}, "(x1,x2)= (",
formatC(x1, width = 4), ",", formatC(x2, width = 4),
")", "--> xTop=", formatC(xTop, width = 8), "\n",
sep = ""
)
}
Xtract <- function(nam, L, default, indx) rep(if (nam %in%
names(L)) {
L[[nam]]
} else {
default
}, length.out = indx)[indx]
asTxt <- function(x) if (is.character(x) || is.expression(x) ||
is.null(x)) {
x
} else {
as.character(x)
}
i <- if (inner || hasP) {
1
} else {
2
}
if (!is.null(nPar)) {
pch <- Xtract("pch", nPar, default = 1L:2, i)
cex <- Xtract("cex", nPar, default = c(1, 1), i)
col <- Xtract("col", nPar, default = par("col"), i)
bg <- Xtract("bg", nPar, default = par("bg"), i)
points(if (horiz) {
cbind(yTop, xTop)
} else {
cbind(xTop, yTop)
},
pch = pch, bg = bg, col = col,
cex = cex
)
}
if (leaflab == "textlike") {
p.col <- Xtract("p.col", nPar, default = "white", i)
}
lab.col <- Xtract("lab.col", nPar,
default = par("col"),
i
)
lab.cex <- Xtract("lab.cex", nPar, default = c(1, 1), i)
lab.font <- Xtract("lab.font", nPar,
default = par("font"),
i
)
lab.xpd <- Xtract("xpd", nPar, default = c(TRUE, TRUE), i)
if (is.leaf(subtree)) {
if (leaflab == "perpendicular") {
if (horiz) {
if (text_pos == 2) {
X <- yTop - dLeaf * lab.cex ##############
} else {
X <- yTop + dLeaf * lab.cex ##############
}
Y <- xTop
srt <- 0
adj <- c(0, 0.5)
}
else {
Y <- yTop - dLeaf * lab.cex
X <- xTop
srt <- 90
adj <- 1
}
nodeText <- asTxt(attr(subtree, "label"))
text(X, Y, nodeText,
xpd = lab.xpd, srt = srt, adj = adj,
cex = lab.cex, col = lab.col, font = lab.font,
pos = text_pos, offset = text_offset
) ###########
}
}
else if (inner) {
segmentsHV <- function(x0, y0, x1, y1) {
if (horiz) {
segments(y0, x0, y1, x1,
col = col, lty = lty,
lwd = lwd
)
} else {
segments(x0, y0, x1, y1,
col = col, lty = lty,
lwd = lwd
)
}
}
for (k in seq_along(subtree)) {
child <- subtree[[k]]
yBot <- attr(child, "height")
if (getOption("verbose")) {
cat("ch.", k, "@ h=", yBot, "; ")
}
if (is.null(yBot)) {
yBot <- 0
}
xBot <- if (center) {
mean(bx$limit[k:(k + 1)])
} else {
bx$limit[k] + .midDend(child)
}
hasE <- !is.null(ePar <- attr(child, "edgePar"))
if (!hasE) {
ePar <- edgePar
}
i <- if (!is.leaf(child) || hasE) {
1
} else {
2
}
col <- Xtract("col", ePar,
default = par("col"),
i
)
lty <- Xtract("lty", ePar,
default = par("lty"),
i
)
lwd <- Xtract("lwd", ePar,
default = par("lwd"),
i
)
if (type == "triangle") {
segmentsHV(xTop, yTop, xBot, yBot)
}
else {
segmentsHV(xTop, yTop, xBot, yTop)
segmentsHV(xBot, yTop, xBot, yBot)
}
vln <- NULL
if (is.leaf(child) && leaflab == "textlike") {
nodeText <- asTxt(attr(child, "label"))
if (getOption("verbose")) {
cat("-- with \"label\"", format(nodeText))
}
hln <- 0.6 * strwidth(nodeText, cex = lab.cex) / 2
vln <- 1.5 * strheight(nodeText, cex = lab.cex) / 2
rect(xBot - hln, yBot, xBot + hln, yBot + 2 *
vln, col = p.col)
text(xBot, yBot + vln, nodeText,
xpd = lab.xpd,
cex = lab.cex, col = lab.col, font = lab.font
) # , pos = text_pos)
}
if (!is.null(attr(child, "edgetext"))) {
edgeText <- asTxt(attr(child, "edgetext"))
if (getOption("verbose")) {
cat("-- with \"edgetext\"", format(edgeText))
}
if (!is.null(vln)) {
mx <- if (type == "triangle") {
(xTop + xBot + ((xTop - xBot) / (yTop - yBot)) *
vln) / 2
} else {
xBot
}
my <- (yTop + yBot + 2 * vln) / 2
}
else {
mx <- if (type == "triangle") {
(xTop + xBot) / 2
} else {
xBot
}
my <- (yTop + yBot) / 2
}
p.col <- Xtract("p.col", ePar,
default = "white",
i
)
p.border <- Xtract("p.border", ePar,
default = par("fg"),
i
)
p.lwd <- Xtract("p.lwd", ePar,
default = lwd,
i
)
p.lty <- Xtract("p.lty", ePar,
default = lty,
i
)
t.col <- Xtract("t.col", ePar,
default = col,
i
)
t.cex <- Xtract("t.cex", ePar, default = 1, i)
t.font <- Xtract("t.font", ePar,
default = par("font"),
i
)
vlm <- strheight(c(edgeText, "h"), cex = t.cex) / 2
hlm <- strwidth(c(edgeText, "m"), cex = t.cex) / 2
hl3 <- c(hlm[1L], hlm[1L] + hlm[2L], hlm[1L])
if (horiz) {
polygon(my + c(-hl3, hl3), mx + sum(vlm) *
c(-1L:1L, 1L:-1L),
col = p.col, border = p.border,
lty = p.lty, lwd = p.lwd
)
text(my, mx, edgeText,
cex = t.cex, col = t.col,
font = t.font
) # , pos = text_pos)
}
else {
polygon(mx + c(-hl3, hl3), my + sum(vlm) *
c(-1L:1L, 1L:-1L),
col = p.col, border = p.border,
lty = p.lty, lwd = p.lwd
)
text(mx, my, edgeText,
cex = t.cex, col = t.col,
font = t.font
)
}
}
# plotNode_horiz
Recall(bx$limit[k], bx$limit[k + 1],
subtree = child, #########
type, center, leaflab, dLeaf, nodePar, edgePar,
horiz, text_pos = text_pos, text_offset = text_offset
) ########
}
}
invisible()
}
#' @title Plotting a left-tip-adjusted horizontal dendrogram
#' @export
#' @description
#' The default \code{plot(dend, horiz = TRUE)}, gives us a dendrogram tree plot
#' with the tips turned right. The current function enables the creation of
#' the same tree, but with the tips turned left. The main challange in doing this
#' is finding the distance of the labels from the leaves tips - which is solved
#' with this function.
#' @param x tree object (dendrogram)
#' @param type a character vector with either "rectangle" or "triangle" (passed to \link{plot.dendrogram})
#' @param center logical; if TRUE, nodes are plotted centered with respect to
#' the leaves in the branch. Otherwise (default), plot them in the
#' middle of all direct child nodes.
#' @param edge.root logical; if true, draw an edge to the root node.
#' @param dLeaf a number specifying the distance in user coordinates between
#' the tip of a leaf and its label. If NULL as per default, 3/4 of a letter
#' width is used.
#' @param horiz logical indicating if the dendrogram should be
#' drawn horizontally or not. In this function it MUST be TRUE!
#' @param xaxt graphical parameters, or arguments for other methods.
#' @param yaxt graphical parameters, or arguments for other methods.
#' @param xlim (NULL) optional x- and y-limits of the plot, passed to plot.default.
#' The defaults for these show the full dendrogram.
#' @param ylim (NULL) optional x- and y-limits of the plot, passed to plot.default.
#' The defaults for these show the full dendrogram.
#' @param nodePar NULL.
#' @param edgePar list()
#' @param leaflab c("perpendicular", "textlike", "none")
#' @param side logical (TRUE). Should the tips of the drawn tree be facing
#' the left side. This is the important feature of this function.
#' @param text_pos integer from either 1 to 4 (2). Two relevant values
#' are 2 and 4. 2 (default) means that the labels are alligned to the
#' tips of the tree leaves. 4 will have the labels allign to the left,
#' making them look like they were when the tree was on the left side
#' (with leaves tips facing to the right).
#' @param ... passed to \link{plot}.
#' @return The invisiable dLeaf value.
#' @source
#' This function is based on replicating \link{plot.dendrogram}.
#' In fact, I'd be happy if in the future, some tweaks could be make to
#' \link{plot.dendrogram}, so that it would replace the need for this function.
#'
#' @seealso \link{plot.dendrogram}, \link{tanglegram}
#' @examples
#' \dontrun{
#' dend <- USArrests[1:10, ] %>%
#' dist() %>%
#' hclust() %>%
#' as.dendrogram()
#'
#' par(mfrow = c(1, 2), mar = rep(6, 4))
#' plot_horiz.dendrogram(dend, side = FALSE)
#' plot_horiz.dendrogram(dend, side = TRUE)
#' # plot_horiz.dendrogram(dend, side=TRUE, dLeaf= 0)
#' # plot_horiz.dendrogram(dend, side=TRUE, nodePar = list(pos = 1))
#' # sadly, lab.pos is not implemented yet,
#' ## so the labels can not be right aligned...
#'
#'
#' plot_horiz.dendrogram(dend, side = F)
#' plot_horiz.dendrogram(dend, side = TRUE, dLeaf = 0, xlim = c(100, -10)) # bad
#' plot_horiz.dendrogram(dend, side = TRUE, text_offset = 0)
#' plot_horiz.dendrogram(dend, side = TRUE, text_offset = 0, text_pos = 4)
#' }
plot_horiz.dendrogram <- function(x,
type = c("rectangle", "triangle"),
center = FALSE,
edge.root = is.leaf(x) || !is.null(attr(x, "edgetext")),
dLeaf = NULL,
horiz = TRUE,
xaxt = "n", yaxt = "s",
xlim = NULL, ylim = NULL,
nodePar = NULL, edgePar = list(),
leaflab = c(
"perpendicular",
"textlike", "none"
),
side = TRUE,
text_pos = 2,
...) {
# reproduces plot.dendrogram in order to set the correct
# strwidth for the labels when using revers horiz!
# @param side logical (FALSE). To which direction should the dendrogram turn.
# if FALSE (default) then we will get the standard left side dendrogram.
# if TRUE, then we will have a right turning dendrogram.
if (!is.dendrogram(x)) x <- as.dendrogram(x)
if (!horiz) stop("This function was created ONLY for horiz==TRUE.")
# if NOT side - then plot as usual
if (!side) {
plot(x,
center = center,
type = type, nodePar = nodePar, edgePar = edgePar, leaflab = leaflab,
edge.root = edge.root,
dLeaf = dLeaf,
horiz = horiz,
xaxt = xaxt, yaxt = yaxt,
xlim = xlim, ylim = ylim, ...
)
return(invisible(NULL))
}
#######################
### The same as:
#### plot.dendrogram
type <- match.arg(type)
leaflab <- match.arg(leaflab)
hgt <- attr(x, "height")
if (edge.root && is.logical(edge.root)) {
edge.root <- 0.0625 * if (is.leaf(x)) {
1
} else {
hgt
}
}
mem.x <- stats_.memberDend(x)
yTop <- hgt + edge.root
if (center) {
x1 <- 0.5
x2 <- mem.x + 0.5
}
else {
x1 <- 1
x2 <- mem.x
}
xl. <- c(x1 - 1 / 2, x2 + 1 / 2)
yl. <- c(0, yTop)
if (horiz) {
tmp <- xl.
xl. <- rev(yl.)
yl. <- tmp
tmp <- xaxt
xaxt <- yaxt
yaxt <- tmp
}
if (missing(xlim) || is.null(xlim)) {
xlim <- xl.
}
if (missing(ylim) || is.null(ylim)) {
ylim <- yl.
}
dev.hold()
on.exit(dev.flush())
#######################
### NEW code
# for right_side
# if(side) {
xlim <- rev(xlim)
plot(0,
xlim = xlim, ylim = ylim, type = "n", xlab = "",
ylab = "", xaxt = xaxt, yaxt = yaxt, frame.plot = FALSE, ...
) # , axes = FALSE)
labels_x <- labels(x)
max_labels_x <- labels_x[which.max(nchar(labels_x))]
base_dLeaf <- strwidth(max_labels_x)
if (is.null(dLeaf)) {
if (text_pos == 2) {
dLeaf <- 0.75 * strwidth("w")
} else {
dLeaf <- -0.75 * strwidth("w") - base_dLeaf
}
### (if (horiz) else strheight("x")) ## this function gives ONLY horiz= TRUE
} else {
if (text_pos != 2) dLeaf <- dLeaf - base_dLeaf
}
# par(new=TRUE)
# } # else {
# # the usual stuff...
# plot(x,
# horiz=horiz,
# center = center,
# edge.root = edge.root,
# dLeaf = dLeaf,
# xaxt = yaxt, yaxt = xaxt, # these are reversed in order to be re-reversed later due to the horiz=TRUE in this function...
# xlim=xlim, ylim=ylim,
# ...)
# if(side) par(new=FALSE)
###### back to the function as usual:
if (edge.root) {
x0 <- stats_plotNodeLimit(x1, x2, x, center)$x
if (horiz) {
segments(hgt, x0, yTop, x0)
} else {
segments(x0, hgt, x0, yTop)
}
if (!is.null(et <- attr(x, "edgetext"))) {
my <- mean(hgt, yTop)
if (horiz) {
text(my, x0, et)
} else {
text(x0, my, et)
}
}
}
# stats_plotNode
# @param text_offset Numeric (NULL). This value gives the offset of the label
# from the specified coordinate in fractions of a character width.
# If NULL (default) then 3/4 of a letter width is used.
#
# This number overrides dLeaf.
plotNode_horiz(x1, x2, x,
type = type, center = center, leaflab = leaflab,
dLeaf = dLeaf, nodePar = nodePar, edgePar = edgePar,
horiz = horiz, text_pos = text_pos
)
return(invisible(dLeaf))
}
# # stats_plot.dendrogram
# # stats_plotNode
#' @title Tanglegram plot
#' @export
#' @rdname tanglegram
#' @description
#' Plots a tanglegram plot of a side by side trees.
#'
#' @author Tal Galili, Johan Renaudie
#'
#'
#' @param dend1 tree object (dendrogram/dendlist/hclust/phylo), plotted on the left
#' @param dend2 tree object (dendrogram/hclust/phylo), plotted on the right
#' @param which an integer vector of length 2, indicating
#' which of the trees in the dendlist object should be plotted
#' @param sort logical (FALSE). Should the dendrogram's labels be "sorted"?
#' (might give a better tree in some cases).
#' @param color_lines a vector of colors for the lines connected the labels.
#' If the colors are shorter than the number of labels, they are recycled
#' (and a warning is issued).
#' The colors in the vector are applied on the lines from the bottom up.
#' @param lwd width of the lines connecting the labels. (default is 3.5)
#' @param edge.lwd width of the dendrograms lines. Default is NULL.
#' If set, then it switches `highlight_branches_lwd` to FALSE. If you want thicker
#' lines which reflect the height, please use \link{highlight_branches_lwd} on the
#' dendrograms/dendlist.
#' @param columns_width a vector with three elements, giving the relative
#' sizes of the the three plots (left dendrogram, connecting lines,
#' right dendrogram). This is passed to \link{layout} if parameter just_one is TRUE.
#' The default is: c(5,3,5)
#' @param margin_top the number of lines of margin to be specified on the top
#' of the plots.
#' @param margin_bottom the number of lines of margin to be specified on the
#' bottom of the plots.
#' @param margin_inner margin_bottom the number of lines of margin
#' to be specified on the inner distence between the dendrograms
#' and the connecting lines.
#' @param margin_outer margin_bottom the number of lines of margin
#' to be specified on the outer distence between the dendrograms
#' and the connecting lines.
#' @param left_dendo_mar mar parameters of the left dendrgoram.
#' @param right_dendo_mar mar parameters of the right dendrgoram.
#' @param intersecting logical (TRUE). Should the leaves of the two dendrograms
#' be pruned so that the two trees will have the same labels?
#' @param dLeaf a number specifying the distance in user coordinates between
#' the tip of a leaf and its label. If NULL, as per default,
#' 3/4 of a letter width or height is used.
#'
#' Notice that if we are comparing two dendrograms with different
#' heights, manually changing dLeaf will affect both trees differently.
#' In such a case, it is recommanded to manually change dLeaf_left
#' and dLeaf_right.
#' This can be especially important when changing the lab.cex of the
#' dendrogram's labels.
#' Alternatively, one could manually set the xlim parameter for both
#' trees, which will force the proportion of distances of the
#' labels from the trees to remain the same.
#'
#' @param dLeaf_left dLeaf of the left dendrogram, by default it is equal to dLeaf (often negative).
#' @param dLeaf_right dLeaf of the right dendrogram, by default it is equal to minus dLeaf (often positive).
#' @param axes logical (TRUE). Should plot axes be plotted?
#' @param type type of plot ("t"/"r" = triangle or rectangle)
#' @param lab.cex numeric scalar, influanicing the cex size of the labels.
#' @param remove_nodePar logical (FALSE). Should the nodePar of the leaves be
#' removed? (useful when the trees' leaves has too many parameters on them)
#' @param main Character. Title above the connecting lines.
#' @param main_left Character. Title of the left dendrogram.
#' @param main_right Character. Title of the right dendrogram.
#' @param sub Character. Title below the connecting lines.
#' @param k_labels integer. Number of groups by which to color the leaves.
#' @param k_branches integer. Number of groups by which to color the branches.
#' @param rank_branches logical (FALSE). Should the branches heights be adjusted?
#' (setting this to TRUE - can make it easier for
#' comparing topological differences)
#' @param hang logical (FALSE). Should we hang the leaves of the trees?
#' @param match_order_by_labels logical (TRUE). Should the leaves value order
#' be matched between the two trees based on labels? This is a MUST in order
#' to have the lines connect the correct labels. Set this to FALSE if you
#' want to make the plotting a bit faster, and only after you are sure
#' the labels and orders are correctly aligned.
#' @param cex_main A numerical value giving the amount by which plotting title
#' should be magnified relative to the default.
#' @param cex_main_left see cex_main.
#' @param cex_main_right see cex_main.
#' @param cex_sub see cex_main.
#' @param highlight_distinct_edges logical (default is TRUE). If to highlight distinct edges in each tree (by changing their line types to 2).
#' (notice that this can be slow on large trees)
#'
#' This parameter will automatically be turned off if the tree already comes with a "lty" edgePar
#' (this is checked using \link{has_edgePar}). A "lty" can be removed by using set("clear_branches"), by
#' removing all of the edgePar parameters of the dendrogram.
#'
#' @param common_subtrees_color_lines logical (default is TRUE). color the connecting line based on the common subtrees of both dends.
#' This only works if
#' (notice that this can be slow on large trees)
#' @param common_subtrees_color_lines_default_single_leaf_color When representing edges between common subtrees
#' (i.e. common_subtrees_color_branches = TRUE), this parameter sets the color of edges for subtrees that are NOT common.
#' Default is "grey"
#' @param common_subtrees_color_branches logical (default is FALSE).
#' Color the branches of both dends based on the common subtrees.
#' (notice that this can be slow on large trees)
#' This is FALSE by default since it will override the colors of the existing tree.
#' @param highlight_branches_col logical (default is FALSE). Should \link{highlight_branches_col} be used on the dendrograms.
#'
#' This parameter will automatically be turned off if the tree already comes with a "col" edgePar
#' (this is checked using \link{has_edgePar}). A "lty" can be removed by using set("clear_branches"), by
#' removing all of the edgePar parameters of the dendrogram.
#'
#' @param highlight_branches_lwd logical (default is TRUE). Should \link{highlight_branches_lwd} be used on the dendrograms.
#'
#' This parameter will automatically be turned off if the tree already comes with a "lwd" edgePar
#' (this is checked using \link{has_edgePar}). A "lty" can be removed by using set("clear_branches"), by
#' removing all of the edgePar parameters of the dendrogram.
#'
#' @param faster logical (FALSE). If TRUE, it overrides some other parameters to
#' have them turned off so that the plotting will go a tiny bit faster.
#' @param just_one logical (TRUE). If FALSE, it means at least two tanglegrams
#' will be plotted on the same page and so \link{layout} is not passed.
#' See: \url{https://stackoverflow.com/q/39784746/4137985}
#' @param ... not used.
#' @details
#' Notice that tanglegram does not "resize" well. In case you are resizing your
#' window you would need to re-run the function.
#'
#' @return An invisible \link{dendlist}, with two trees after being
#' modified during the creation of the tanglegram.
#' @source
#' The function is based on code from Johan Renaudie (plannapus), after major revisions. See:
#' \url{https://stackoverflow.com/questions/12456768/duelling-dendrograms-in-r-placing-dendrograms-back-to-back-in-r}
#'
#' As far as I could tell, this code was originally inspired by Dylan Beaudette
#' function \code{dueling.dendrograms} from the sharpshootR package:
#' \url{https://CRAN.R-project.org/package=sharpshootR}
#' tanglegram
#' @seealso \link{remove_leaves_nodePar}, \link{plot_horiz.dendrogram}, \link{rank_branches},
#' \link{hang.dendrogram}
#' @examples
#' \dontrun{
#' set.seed(23235)
#' ss <- sample(1:150, 10)
#' dend1 <- iris[ss, -5] %>%
#' dist() %>%
#' hclust("com") %>%
#' as.dendrogram()
#' dend2 <- iris[ss, -5] %>%
#' dist() %>%
#' hclust("sin") %>%
#' as.dendrogram()
#' dend12 <- dendlist(dend1, dend2)
#'
#' dend12 %>% tanglegram()
#'
#' tanglegram(dend1, dend2)
#' tanglegram(dend1, dend2, sort = TRUE)
#' tanglegram(dend1, dend2, remove_nodePar = TRUE)
#' tanglegram(dend1, dend2, k_labels = 6, k_branches = 4)
#'
#' tanglegram(dend1, dend2,
#' lab.cex = 2, edge.lwd = 3,
#' margin_inner = 5, type = "t", center = TRUE
#' )
#'
#'
#' ## works nicely:
#' tanglegram(dend1, dend2,
#' lab.cex = 2, edge.lwd = 3,
#' margin_inner = 3.5, type = "t", center = TRUE,
#' dLeaf = -0.1, xlim = c(7, 0),
#' k_branches = 3
#' )
#'
#'
#' # using rank_branches can make the comparison even easier
#' tanglegram(rank_branches(dend1), rank_branches(dend2),
#' lab.cex = 2, edge.lwd = 3,
#' margin_inner = 3.5, type = "t", center = TRUE,
#' dLeaf = -0.1, xlim = c(5.1, 0), columns_width = c(5, 1, 5),
#' k_branches = 3
#' )
#'
#'
#'
#' ########
#' ## Nice example of some colored trees
#'
#' # see the coloring of common sub trees:
#' set.seed(23235)
#' ss <- sample(1:150, 10)
#' dend1 <- iris[ss, -5] %>%
#' dist() %>%
#' hclust("com") %>%
#' as.dendrogram()
#' dend2 <- iris[ss, -5] %>%
#' dist() %>%
#' hclust("sin") %>%
#' as.dendrogram()
#' dend12 <- dendlist(dend1, dend2)
#' # dend12 %>% untangle %>% tanglegram
#' dend12 %>% tanglegram(common_subtrees_color_branches = TRUE)
#'
#'
#' set.seed(22133513)
#' ss <- sample(1:150, 10)
#' dend1 <- iris[ss, -5] %>%
#' dist() %>%
#' hclust("com") %>%
#' as.dendrogram()
#' dend2 <- iris[ss, -5] %>%
#' dist() %>%
#' hclust("sin") %>%
#' as.dendrogram()
#' dend12 <- dendlist(dend1, dend2)
#' # dend12 %>% untangle %>% tanglegram
#' dend12 %>% tanglegram(common_subtrees_color_branches = TRUE)
#' dend12 %>% tanglegram()
#' }
tanglegram <- function(dend1, ...) {
UseMethod("tanglegram")
}
#' @export
#' @rdname tanglegram
tanglegram.default <- function(dend1, ...) {
stop("No default function for tanglegram - must use a dendrogram/hclust/phylo object")
}
#' @export
#' @rdname tanglegram
tanglegram.hclust <- function(dend1, ...) {
tanglegram.dendrogram(dend1 = dend1, ...)
}
#' @export
#' @rdname tanglegram
tanglegram.phylo <- function(dend1, ...) {
tanglegram.dendrogram(dend1 = dend1, ...)
}
#' @export
#' @rdname tanglegram
tanglegram.dendlist <- function(dend1, which = c(1L, 2L), main_left, main_right, just_one = TRUE, ...) {
# many things can go wrong here (which we might wish to fix):
# we could have parameter just_one set to FALSE but no layout predefined, in which case we can't plot
if (!just_one & identical(par("mfrow"), c(1, 1))) stop("A layout must be defined when just_one is FALSE")
# we could get a dendlist with a length of 1 - in which case, we can't plot
if (length(dend1) == 1) stop("Your dendlist has only 1 dendrogram - a tanglegram can not be plotted")
# we could get a dendlist with a length of >2 - in which case, should we only plot the first two items?
if (all(which %in% seq_len(length(dend1)))) {
l1 <- which[1]
l2 <- which[2]
if (!is.null(names(dend1))) {
if (missing(main_left)) main_left <- names(dend1)[l1]
if (missing(main_right)) main_right <- names(dend1)[l2]
} else {
if (missing(main_left)) main_left <- ""
if (missing(main_right)) main_right <- ""
}
tanglegram.dendrogram(dend1[[l1]], dend1[[l2]], main_left = main_left, main_right = main_right, just_one = just_one, ...)
} else {
stop("You are trying to plot trees which are outside the range of trees in your dendlist")
}
}
#' @export
#' @rdname tanglegram
tanglegram.dendrogram <- function(dend1, dend2, sort = FALSE,
color_lines,
lwd = 3.5,
edge.lwd = NULL,
# columns_width = c(5, 2, 3, 2, 5),
columns_width = c(5, 3, 5),
margin_top = 3,
margin_bottom = 2.5,
margin_inner = 3,
margin_outer = 0.5,
left_dendo_mar = c(margin_bottom, margin_outer, margin_top, margin_inner),
right_dendo_mar = c(margin_bottom, margin_inner, margin_top, margin_outer),
intersecting = TRUE,
dLeaf = NULL, # -.3,
dLeaf_left = dLeaf,
dLeaf_right = dLeaf,
axes = TRUE,
type = "r", # can also be "t"
lab.cex = NULL,
remove_nodePar = FALSE,
main = "",
main_left = "",
main_right = "",
sub = "",
k_labels = NULL,
k_branches = NULL,
rank_branches = FALSE,
hang = FALSE,
match_order_by_labels = TRUE,
cex_main = 2,
cex_main_left = cex_main,
cex_main_right = cex_main,
cex_sub = cex_main,
highlight_distinct_edges = TRUE,
common_subtrees_color_lines = TRUE,
common_subtrees_color_lines_default_single_leaf_color = "grey",
common_subtrees_color_branches = FALSE,
highlight_branches_col = FALSE,
highlight_branches_lwd = TRUE,
faster = FALSE,
just_one = TRUE,
...) {
if (faster) {
highlight_distinct_edges <- FALSE
common_subtrees_color_lines <- FALSE
common_subtrees_color_branches <- FALSE
highlight_branches_lwd <- FALSE
}
if (just_one) {
# save default, for resetting...
def_par <- par(no.readonly = TRUE)
}
# characters_to_prune = the number of characters to leave after pruning the labels.
# remove_nodePar = makes sure that we won't have any dots at the end of leaves
if (!is.dendrogram(dend1)) dend1 <- as.dendrogram(dend1)
if (!is.dendrogram(dend2)) dend2 <- as.dendrogram(dend2)
# remove colors from the tips of leaves
if (remove_nodePar) {
dend1 <- remove_leaves_nodePar(dend1)
dend2 <- remove_leaves_nodePar(dend2)
}
# sort them for better graph
if (sort == TRUE) { # based on the "rotate.dendrogram" function
dend1 <- sort(dend1)
dend2 <- sort(dend2)
}
if (intersecting) {
dend12 <- intersect_trees(dend1, dend2, warn = TRUE)
dend1 <- dend12[[1]]
dend2 <- dend12[[2]]
}
# adjust labels cex:
if (!is.null(lab.cex)) {
dend1 <- assign_values_to_leaves_nodePar(dend1, lab.cex, "lab.cex", warn = dendextend_options("warn"))
dend2 <- assign_values_to_leaves_nodePar(dend2, lab.cex, "lab.cex", warn = dendextend_options("warn"))
}
if (!is.null(edge.lwd)) {
highlight_branches_lwd <- FALSE # so that it does not override this parameter
dend1 <- assign_values_to_branches_edgePar(dend1, edge.lwd, "lwd")
dend2 <- assign_values_to_branches_edgePar(dend2, edge.lwd, "lwd")
}
if (!is.null(k_labels)) {
dend1 <- color_labels(dend1, k = k_labels)
dend2 <- color_labels(dend2, k = k_labels)
}
if (!is.null(k_branches)) {
dend1 <- color_branches(dend1, k = k_branches)
dend2 <- color_branches(dend2, k = k_branches)
}
if (rank_branches) {
dend1 <- rank_branches(dend1)
dend2 <- rank_branches(dend2)
}
# MUST
if (hang) {
dend1 <- hang.dendrogram(dend1)
dend2 <- hang.dendrogram(dend2)
}
if (highlight_distinct_edges) {
##
if (!has_edgePar(dend1, "lty")) dend1 <- highlight_distinct_edges(dend1, dend2, edgePar = "lty", value = 3)
if (!has_edgePar(dend2, "lty")) dend2 <- highlight_distinct_edges(dend2, dend1, edgePar = "lty", value = 3)
}
if (common_subtrees_color_branches) {
clusters1 <- common_subtrees_clusters(dend1, dend2)
# clusters2 <- common_subtrees_clusters(dend2, dend1)
dend1 <- color_branches(dend1, clusters = clusters1)
# dend2 <- color_branches(dend2, clusters = clusters2)
dend1_leaves_colors <- get_leaves_branches_col(dend1)
# in cases when lwd is defined, the NAs are not provided and the two vectors
# (clusters1 and dend1_leaves_colors) have different lengths.
# I repeat this to all cases by removing the NAs. Knowing where they should be,
# based on the 0s in clusters1, I am able to fit the colors properly in both cases.
dend1_leaves_colors <- as.vector(na.omit(dend1_leaves_colors))
tmp <- clusters1
tmp[tmp != 0] <- dend1_leaves_colors
dend1_leaves_colors <- tmp
dend1_leaves_colors[tmp == 0] <- "black"
# match_1_to_be_2
ss <- match(labels(dend2), labels(dend1))
# labels(dend1)[ss]
# labels(dend2)
the_leaves_colors <- dend1_leaves_colors[ss]
# the_leaves_colors[is.na(the_leaves_colors)] <- 1
dend2_clusters <- rank_values_with_clusters(clusters1[ss], ignore0 = TRUE)
dend2 <- branches_attr_by_clusters(dend2, dend2_clusters,
values = the_leaves_colors, attr = "col",
branches_changed_have_which_labels = "all"
)
# tanglegram(dend1,dend2)
# a <- clusters1[ss]
# a[c(1,2,6)] <- 4:6
# b <- dend1_leaves_colors[ss]
# b[is.na(b)] <- "black"
# branches_attr_by_clusters(dend2, a,
# values = b, attr = "col")
# If I know I am using the common_subtrees_color_branches
# I might as well match them to the lines:
if (common_subtrees_color_lines) {
color_lines <- dend1_leaves_colors
color_lines[is.na(color_lines)] <- common_subtrees_color_lines_default_single_leaf_color
}
}
# if we didn't resolve color_lines yet - let's figure it out now:
if (missing(color_lines)) {
if (common_subtrees_color_lines) {
# color_lines <- rep("black", nleaves(dend1))
# lines_color_clusters <- common_subtrees_clusters(dend1, dend2, leaves_get_0_cluster = TRUE)
# ss_not_0s <- lines_color_clusters != 0
# colors_for_lines_color <- lines_color_clusters[ss_not_0s] %>% unique %>% length %>% rainbow_fun
# color_lines[ss_not_0s] <- colors_for_lines_color[lines_color_clusters[ss_not_0s]]
lines_color_clusters <- common_subtrees_clusters(dend1, dend2, leaves_get_0_cluster = FALSE)
colors_for_lines_color <- lines_color_clusters %>%
unique() %>%
length() %>%
rainbow_fun()
color_lines <- colors_for_lines_color[lines_color_clusters]
ss_0s <- replace_unique_items_with_0_and_rank(lines_color_clusters) == 0
color_lines[ss_0s] <- common_subtrees_color_lines_default_single_leaf_color
} else {
color_lines <- "darkgrey"
}
}
if (highlight_branches_col) {
if (!has_edgePar(dend1, "col")) dend1 <- highlight_branches_col(dend1)
if (!has_edgePar(dend2, "col")) dend2 <- highlight_branches_col(dend2)
}
if (highlight_branches_lwd) {
if (!has_edgePar(dend1, "lwd")) dend1 <- highlight_branches_lwd(dend1)
if (!has_edgePar(dend2, "lwd")) dend2 <- highlight_branches_lwd(dend2)
}
l <- nleaves(dend1)
# makes sure that dLeaf gives a symmetric result.
if (!is.null(dLeaf) && dLeaf_right == dLeaf_left) {
dLeaf_right <- -dLeaf_left
}
##########################################
##### Plotting.
##########################################
labels_dend1 <- labels(dend1)
max_labels_dend1 <- labels_dend1[which.max(nchar(labels_dend1))]
# The matrix to draw the arrows:
if (match_order_by_labels) dend1 <- match_order_by_labels(dend1, dend2)
ord_arrow <- cbind((1:l)[order(order.dendrogram(dend1))], (1:l)[order(order.dendrogram(dend2))])
# Set the layout of the plot elements
if (just_one) layout(matrix(1:3, nrow = 1), widths = columns_width)
#################
# The first dendrogram:
#################
par(mar = left_dendo_mar)
plot(dend1,
horiz = TRUE, ylim = c(0, l),
dLeaf = dLeaf_left,
type = type, axes = axes,
main = main_left,
cex.main = cex_main_left,
# ...)
# leaflab="none",
yaxs = "r", xaxs = "i", ...
) # this might be causing bugs when refreshing a resized window.
# now that I have a plot to use, I can calculate strwidth
# this ASSUMES that both tree plots are of the same size/shape...
#################
# The arrows:
#################
# arros colors:
if (length(color_lines) < l) color_lines <- rep.int(color_lines, l)
color_lines <- color_lines[ord_arrow[, 1]]
par(mar = c(margin_bottom, 0, margin_top, 0))
plot(NA,
bty = "n", axes = FALSE, xlim = c(0, 1), ylim = c(0, l), ylab = "", xlab = "", # )#,
yaxs = "r", xaxs = "i"
)
col_indx <- 0
apply(
ord_arrow, 1,
function(x) {
col_indx <<- col_indx + 1
arrows(0, x[1], 1, x[2], code = 0, length = 0.05, col = color_lines[col_indx], lwd = lwd)
}
)
mtext(main, side = 3, cex = cex_main)
mtext(sub, side = 1, cex = cex_sub)
#################
# And the second dendrogram (to reverse it I reversed the xlim vector:
#################
par(mar = right_dendo_mar)
plot_horiz.dendrogram(dend2,
side = TRUE, dLeaf = dLeaf_right,
type = type, axes = axes,
ylim = c(0, l),
cex.main = cex_main_left,
main = main_right,
# ...)
# leaflab="none",
yaxs = "r", xaxs = "i", ...
)
# layout(matrix(1)) # not required
if (just_one) {
par(def_par) #- reset to default
}
return(invisible(dendlist(dend1 = dend1, dend2 = dend2)))
}
# add an "abbreviation" parameter - to prune the labels of two trees.
#' @export
#' @rdname tanglegram
dendbackback <- tanglegram.dendrogram # another name for the same function.
# hclustbackback <- tanglegram.hclust # another name for the same function.
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