How can I plot a tree (and squirrels) in R?

Question

Here is my tree:

tree = data.frame(branchID = c(1,11,12,111,112,1121,1122), length = c(32, 21, 19, 5, 12, 6, 2))

> tree
  branchID length
1        1              


        

Answer 1

I probably over-thought this, but... squirrels.

get.coords <- function(a, d, x0, y0) {
  a <- ifelse(a <= 90, 90 - a, 450 - a)
  data.frame(x = x0 + d * cos(a / 180 * pi), 
             y = y0+ d * sin(a / 180 * pi))
}


tree$angle <- sapply(gsub(2, '+45', gsub(1, '-45', tree$branchID)), 
                     function(x) eval(parse(text=x)))
tree$tipy <- tree$tipx <- tree$basey <- tree$basex <- NA

for(i in seq_len(nrow(tree))) {
  if(tree$branchID[i] == 0) {
    tree$basex[i] <- tree$basey[i] <- tree$tipx[i] <- 0
    tree$tipy[i] <- tree$length[i]
    next
  } else if(tree$branchID[i] %in% 1:2) {
    parent <- 0
  } else {
    parent <- substr(tree$branchID[i], 1, nchar(tree$branchID[i])-1)
  }
  tree$basex[i] <- tree$tipx[which(tree$branchID==parent)]
  tree$basey[i] <- tree$tipy[which(tree$branchID==parent)]
  tip <- get.coords(tree$angle[i], tree$length[i], tree$basex[i], tree$basey[i])
  tree$tipx[i] <- tip[, 1]
  tree$tipy[i] <- tip[, 2]
}  

squirrels$nesty <- squirrels$nestx <- NA
for (i in seq_len(nrow(squirrels))) {
  b <- tree[tree$branchID == squirrels$branchID[i], ]
  nest <- get.coords(b$angle, squirrels$PositionOnBranch[i], b$basex, b$basey)
  squirrels$nestx[i] <- nest[1]
  squirrels$nesty[i] <- nest[2]
}

And now we plot.

plot.new()
plot.window(xlim=range(tree$basex, tree$tipx), 
            ylim=range(tree$basey, tree$tipy), asp=1)
with(tree, segments(basex, basey, tipx, tipy, lwd=pmax(10/nchar(branchID), 1)))
points(squirrels[, c('nestx', 'nesty')], pch=21, cex=3, bg='white', lwd=2)
text(squirrels[, c('nestx', 'nesty')], labels=seq_len(nrow(squirrels)), font=2)
legend('bottomleft', legend=paste(seq_len(nrow(squirrels)), squirrels$name), bty='n')

And for kicks we will simulate a bigger tree (and put some apples on it like in Farmville):

twigs <- replicate(50, paste(rbinom(5, 1, 0.5) + 1, collapse=''))
branches <- sort(unique(c(sapply(twigs, function(x) sapply(seq_len(nchar(x)), function(y) substr(x, 1, y))))))
tree <- data.frame(branchID=c(0, branches), length=c(30, sample(10, length(branches), TRUE)), 
                   stringsAsFactors=FALSE)


tree$angle <- sapply(gsub(2, '+45', gsub(1, '-45', tree$branchID)), 
                     function(x) eval(parse(text=x)))
tree$tipy <- tree$tipx <- tree$basey <- tree$basex <- NA

for(i in seq_len(nrow(tree))) {
  if(tree$branchID[i] == 0) {
    tree$basex[i] <- tree$basey[i] <- tree$tipx[i] <- 0
    tree$tipy[i] <- tree$length[i]
    next
  } else if(tree$branchID[i] %in% 1:2) {
    parent <- 0
  } else {
    parent <- substr(tree$branchID[i], 1, nchar(tree$branchID[i])-1)
  }
  tree$basex[i] <- tree$tipx[which(tree$branchID==parent)]
  tree$basey[i] <- tree$tipy[which(tree$branchID==parent)]
  tip <- get.coords(tree$angle[i], tree$length[i], tree$basex[i], tree$basey[i])
  tree$tipx[i] <- tip[, 1]
  tree$tipy[i] <- tip[, 2]
}  

plot.new()
plot.window(xlim=range(tree$basex, tree$tipx), 
            ylim=range(tree$basey, tree$tipy), asp=1)
par(mar=c(0, 0, 0, 0))
with(tree, segments(basex, basey, tipx, tipy, lwd=pmax(20/nchar(branchID), 1)))

apple_branches <- sample(branches, 10)
sapply(apple_branches, function(x) {
  b <- tree[tree$branchID == x, ]
  apples <- get.coords(b$angle, runif(sample(2, 1), 0, b$length), b$basex, b$basey)
  points(apples, pch=20, col='tomato2', cex=2)
})

Answer 2

I put a bit more thought/time into this, and have packaged up some horticultural functions in package trees, here.

With trees, you can:

• generate a random tree design (a random seed, so to speak) with seed();
• sow the seed to give rise to a magnificent tree with germinate();
• add randomly-located leaves (or squirrels) with foliate();
• add squirrels (for example) to specified locations with squirrels(); and
• prune() the tree.

---

# Install the package and set the RNG state
devtools::install_github('johnbaums/trees')
set.seed(1)

Let's fertilise a seed and grow a tree

# Create a tree seed    
s <- seed(70, 10, min.branch.length=0, max.branch.length=4,
          min.trunk.height=5, max.trunk.height=8)

head(s, 10)

#       branch    length
# 1          0 6.3039785
# 2          L 2.8500587
# 3         LL 1.5999775
# 4        LLL 1.3014086
# 5       LLLL 3.0283486
# 6      LLLLL 0.8107690
# 7     LLLLLR 2.8444849
# 8    LLLLLRL 0.4867677
# 9   LLLLLRLR 0.9819541
# 10 LLLLLRLRR 0.5732175

# Germinate the seed
g <- germinate(s, col='peachpuff4')

And add some leaves

leafygreens <- colorRampPalette(paste0('darkolivegreen', c('', 1:4)))(100)
foliate(g, 5000, 4, pch=24:25, col=NA, cex=1.5, bg=paste0(leafygreens, '30'))

Or some squirrels

plot(g, col='peachpuff4')
squirrels(g, 
          branches=c("LLLLRRRL", "LRLRR", "LRRLRLLL", "LRRRLL", "RLLLLLR", 
                     "RLLRL", "RLLRRLRR", "RRRLLRL", "RRRLLRR", "RRRRLR"),
          pos=c(0.22, 0.77, 0.16, 0.12, 0.71, 0.23, 0.18, 0.61, 0.8, 2.71),
          pch=20, cex=2.5)

Plotting @Remi.b's tree and squirrels

g <- germinate(list(trunk.height=32, 
                   branches=c(1, 2, 11, 12, 121, 122),
                   lengths=c(21, 19, 5, 12, 6, 2)), 
              left='1', right='2', angle=40)

xy <- squirrels(g, c(0, 1, 121, 1, 11), pos=c(23, 12, 4, 2, 1), 
               left='1', right='2', pch=21, bg='white', cex=3, lwd=2)
text(xy$x, xy$y, labels=seq_len(nrow(xy)), font=2)
legend('bottomleft', bty='n',
      legend=paste(seq_len(nrow(xy)), 
                   c('FluffyTail', 'Ginger', 'NutCracker', 'SuperSquirrel', 
                     'ChipnDale'), sep='. '))

---

EDIT:

Following @baptiste's hot tip about @ScottChamberlain's rphylopic package, it's time to upgrade those dots to squirrels (though they may resemble coffee beans).

library(rphylopic)
s <- seed(50, 10, min.branch.length=0, max.branch.length=5,
          min.trunk.height=5, max.trunk.height=8)
g <- germinate(s, trunk.width=15, col='peachpuff4')
leafygreens <- colorRampPalette(paste0('darkolivegreen', c('', 1:4)))(100)
foliate(g, 2000, 4, pch=24:25, col=NA, cex=1.2, bg=paste0(leafygreens, '50'))
xy <- foliate(g, 2, 2, 4, xy=TRUE, plot=FALSE)

# snazzy drop shadow
add_phylopic_base(
    image_data("5ebe5f2c-2407-4245-a8fe-397466bb06da", size = "64")[[1]], 
    1, xy$x, xy$y, ysize = 2.3, col='black')
add_phylopic_base(
    image_data("5ebe5f2c-2407-4245-a8fe-397466bb06da", size = "64")[[1]], 
    1, xy$x, xy$y, ysize = 2, col='darkorange3')

Answer 3

A version that supports trees with more than two branches. A bit work is required to convert to a data.tree structure, and to add the squirrels to it. But once you're there, the plotting is straight forward.

df <- data.frame(branchID = c(1,11,12,13, 14, 111,112,1121,1122), length = c(32, 21, 12, 8, 19, 5, 12, 6, 2))
squirrels <- data.frame(branchID = c(1,11,1121,11,111), PositionOnBranch = c(23, 12, 4, 2, 1), squirrel=c("FluffyTail", "Ginger", "NutCracker", "SuperSquirrel", "ChipnDale"), stringsAsFactors = FALSE)

library(magrittr)

#derive pathString from branchID, so we can convert it to data.tree structure
df$branchID %>%
  as.character %>%
  sapply(function(x) strsplit(x, split = "")) %>%
  sapply(function(x) paste(x, collapse = "/")) ->
  df$pathString

df$type <- "branch"

library(data.tree)

tree <- FromDataFrameTable(df)

#climb, little squirrels!
for (i in 1:nrow(squirrels)) {
  squirrels[i, 'branchID'] %>%
    as.character %>%
    strsplit(split = "") %>%
    extract2(1) %>%
    extract(-1) -> path
  if (length(path) > 0) branch <- tree$Climb(path)
  else branch <- tree
  #actually, we add the squirrels as branches to our tree
  #What a symbiotic coexistence!
  #advantage: Our SetCoordinates can be re-used as is
  #disadvantage: may be confusing, and it requires us
  #to do some filtering later
  branch$AddChild(squirrels[i, 'squirrel'],
                 length = squirrels[i, 'PositionOnBranch'],
                 type = "squirrel")
}



SetCoordinates <- function(node, branch) {
  if (branch$isRoot) {
    node$x0 <- 0
    node$y0 <- 0
  } else {
    node$x0 <- branch$parent$x1
    node$y0 <- branch$parent$y1
  }

  #let's hope our squirrels didn't flunk in trigonometry ;-)
  angle <- branch$position / (sum(Get(branch$siblings, "type") == "branch") + 2)
  x <- - node$length * cospi(angle)
  y <- sqrt(node$length^2 - x^2)
  node$x1 <- node$x0 + x
  node$y1 <- node$y0 + y
}

#let it grow!
tree$Do(function(node) {
          SetCoordinates(node, node)
          node$lwd <- 10 * (node$root$height - node$level + 1) / node$root$height
        }, filterFun = function(node) node$type == "branch")
tree$Do(function(node) SetCoordinates(node, node$parent), filterFun = function(node) node$type == "squirrel")

Looking at the data:

print(tree, "type", "length", "x0", "y0", "x1", "y1")

This prints like so:

                    levelName     type length        x0       y0         x1       y1
1  1                            branch     32   0.00000  0.00000   0.000000 32.00000
2   ¦--1                        branch     21   0.00000 32.00000 -16.989357 44.34349
3   ¦   ¦--1                    branch      5 -16.98936 44.34349 -19.489357 48.67362
4   ¦   ¦   °--ChipnDale      squirrel      1 -16.98936 44.34349 -17.489357 45.20952
5   ¦   ¦--2                    branch     12 -16.98936 44.34349 -10.989357 54.73580
6   ¦   ¦   ¦--1                branch      6 -10.98936 54.73580 -13.989357 59.93195
7   ¦   ¦   ¦   °--NutCracker squirrel      4 -10.98936 54.73580 -12.989357 58.19990
8   ¦   ¦   °--2                branch      2 -10.98936 54.73580  -9.989357 56.46785
9   ¦   ¦--Ginger             squirrel     12   0.00000 32.00000  -9.708204 39.05342
10  ¦   °--SuperSquirrel      squirrel      2   0.00000 32.00000  -1.618034 33.17557
11  ¦--2                        branch     12   0.00000 32.00000  -3.708204 43.41268
12  ¦--3                        branch      8   0.00000 32.00000   2.472136 39.60845
13  ¦--4                        branch     19   0.00000 32.00000  15.371323 43.16792
14  °--FluffyTail             squirrel     23   0.00000  0.00000   0.000000 23.00000

Once we're here, plotting is also easy:

plot(c(min(tree$Get("x0")), max(tree$Get("x1"))),
     c(min(tree$Get("y0")), max(tree$Get("y1"))),
     type='n', asp=1, axes=FALSE, xlab='', ylab='')

tree$Do(function(node) segments(node$x0, node$y0, node$x1, node$y1, lwd = node$lwd),
        filterFun = function(node) node$type == "branch")

tree$Do(function(node) {
          points(node$x1, node$y1, lwd = 8, col = "saddlebrown")
          text(node$x1, node$y1, labels = node$name, pos = 2, cex = 0.7)
        },
        filterFun = function(node) node$type == "squirrel")

Answer 4

Well, you could convert your data to define a "tree" as defined by the ape package. Here's a function that can convert your data.frame to the correct format.

library(ape)

to.tree <- function(dd) {
    dd$parent <- dd$branchID %/% 10

    root <- subset(dd, parent==0)
    dd <- subset(dd, parent!=0)

    ids <- unique(c(dd$parent, dd$branchID))
    tip <- !(ids %in% dd$parent)
    lvl <- ids[order(!tip, ids)]
    edg <- sapply(dd[,c("parent","branchID")], 
        function(x) as.numeric(factor(x, levels=lvl)))

    x<-list(
        edge=edg,
        edge.length=dd$length,
        tip.label=head(lvl, sum(tip)),
        node.label=tail(lvl, length(tip)-sum(tip)),
        Nnode = length(tip)-sum(tip),
        root.edge=root$length[1]
    )
    class(x)<-"phylo"
    reorder(x)    
}

Then we can plot it somewhat easily

xx <- to.tree(tree)
plot(xx, show.node.label=TRUE, root.edge=TRUE)

Now, if we want to add the squirrel information, we need to know where each branch is located. I'm going to borrow getphylo_x and getphylo_y from this answer. Then I can run

sx<-Vectorize(getphylo_x, "node")(xx, as.character(squirrels$branchID)) -
    tree$length[match(squirrels$branchID, tree$branchID)] +
    squirrels$PositionOnBranch
sy<-Vectorize(getphylo_y, "node")(xx, as.character(squirrels$branchID))

points(sx,sy)
text(sx,sy, squirrels$name, pos=3)

to add the squirrel information to the plot. The final result is

It's not perfect but it's not a bad start.

Answer 5

The reshaping of this might take a while, but this is broadly possible. E.g., rejigging your data representation so it looks like:

library(igraph)
dat <- read.table(text="1 1n2
1n2 1.1
1n2 1.2
1.1 1.1.1
1.1 1.1.2
1.1.2 1.1.2.1
1.1.2 1.1.2.2",header=FALSE)

g <- graph.data.frame(dat)
tkplot(g)

And manually moving the tree parts around in tkplot, you can get:

Doing this automatically is a whole different story admittedly.