ggtree_layouts

# ============================================================
# ggtree Layout Gallery
# Figure 1: Base Layouts
# Figure 2: Derived Layouts (scale & coordinate transforms)
# ============================================================

library(ggplot2)
library(ggtree)
library(ape)
library(patchwork)
library(ggplotify)

# --- Reproducible tree -------------------------------------------------------
set.seed(2017-02-16)
tree <- rtree(50)

# --- Shared theme ------------------------------------------------------------
clean <- theme_void() +
  theme(
    plot.title = element_text(size = 10, face = "bold", hjust = 0.5,
                              margin = margin(t = 2, b = 4)),
    plot.margin = margin(6, 6, 6, 6)
  )

# ============================================================
# FIGURE 1: Base Layouts (12 panels, 4x3)
# ============================================================

p1  <- ggtree(tree) + ggtitle("A") + clean
p2  <- ggtree(tree, layout = "roundrect") + ggtitle("B") + clean
p3  <- ggtree(tree, layout = "slanted") + ggtitle("C") + clean
p4  <- ggtree(tree, layout = "ellipse") + ggtitle("D") + clean
p5  <- ggtree(tree, layout = "circular") + ggtitle("E") + clean
p6  <- ggtree(tree, layout = "fan", open.angle = 120) + ggtitle("F") + clean
p7  <- ggtree(tree, layout = "equal_angle") + ggtitle("G") + clean
p8  <- ggtree(tree, layout = "daylight") + ggtitle("H") + clean
p9  <- ggtree(tree, branch.length = "none") + ggtitle("I") + clean
p10 <- ggtree(tree, layout = "ellipse", branch.length = "none") + ggtitle("J") + clean
p11 <- ggtree(tree, branch.length = "none", layout = "circular") + ggtitle("K") + clean
p12 <- ggtree(tree, layout = "daylight", branch.length = "none") + ggtitle("L") + clean

fig1 <- p1 + p2 + p3 + p4 +
  p5 + p6 + p7 + p8 +
  p9 + p10 + p11 + p12 +
  plot_layout(ncol = 4) +
  plot_annotation(
    title = "ggtree Base Layouts",
    subtitle = paste0(
      "The same 50-tip random tree rendered across twelve layout variants.\n",
      "Top row: rectangular and geometric layouts with branch lengths.\n",
      "Middle row: circular, fan, and unrooted layouts. Bottom row: cladograms (branch.length = 'none')."
    ),
    caption = paste(
      "(A) Rectangular,",
      "(B) roundrect,",
      "(C) slanted,",
      "(D) ellipse,",
      "(E) circular,",
      "(F) fan (open.angle = 120),\n",
      "(G) equal_angle,",
      "(H) daylight,",
      "(I) rectangular cladogram,",
      "(J) ellipse cladogram,",
      "(K) circular cladogram,",
      "(L) daylight cladogram."
    ),
    theme = theme(
      plot.title    = element_text(size = 16, face = "bold", hjust = 0.5,
                                   margin = margin(b = 4)),
      plot.subtitle = element_text(size = 9, hjust = 0.5, color = "grey30",
                                   lineheight = 1.4, margin = margin(b = 10)),
      plot.caption  = element_text(size = 8, hjust = 0, color = "grey40",
                                   lineheight = 1.5, margin = margin(t = 10)),
      plot.margin   = margin(15, 15, 15, 15)
    )
  )

suppressWarnings(
  ggsave("ggtree_base_layouts.png", plot = fig1,
         width = 16, height = 14, dpi = 300, bg = "white")
)

fig1
# ============================================================
# FIGURE 2: Derived Layouts (9 panels, 3x3)
# ============================================================

d_a <- ggtree(tree) + scale_x_reverse() + ggtitle("A") + clean
d_b <- ggtree(tree) + coord_flip() + ggtitle("B") + clean
d_c <- ggtree(tree) + layout_dendrogram() + ggtitle("C") + clean

d_d <- suppressWarnings(
  as.ggplot(ggtree(tree), angle = -30, scale = 0.9)
) + ggtitle("D") + clean

d_e <- ggtree(tree, layout = "slanted") + coord_flip() + ggtitle("E") + clean

d_f <- ggtree(tree, layout = "slanted", branch.length = "none") +
  layout_dendrogram() + ggtitle("F") + clean

d_g <- ggtree(tree, layout = "circular") + xlim(-10, NA) + ggtitle("G") + clean
d_h <- ggtree(tree) + layout_inward_circular() + ggtitle("H") + clean
d_i <- ggtree(tree) + layout_inward_circular(xlim = 15) + ggtitle("I") + clean

fig2 <- d_a + d_b + d_c +
  d_d + d_e + d_f +
  d_g + d_h + d_i +
  plot_layout(ncol = 3) +
  plot_annotation(
    title = "ggtree Derived Layouts",
    subtitle = paste0(
      "The same 50-tip tree transformed via scale, coordinate, and layout functions.\n",
      "These build on base layouts by flipping, rotating, or wrapping the tree."
    ),
    caption = paste(
      "(A) Right-to-left rectangular via scale_x_reverse(),",
      "(B) bottom-up rectangular via coord_flip(),",
      "(C) top-down dendrogram via layout_dendrogram(),\n",
      "(D) rotated rectangular via ggplotify::as.ggplot(angle = -30),",
      "(E) bottom-up slanted via coord_flip(),",
      "(F) top-down cladogram via layout_dendrogram(),\n",
      "(G) circular with expanded xlim,",
      "(H) inward circular via layout_inward_circular(),",
      "(I) inward circular with xlim = 15."
    ),
    theme = theme(
      plot.title    = element_text(size = 16, face = "bold", hjust = 0.5,
                                   margin = margin(b = 4)),
      plot.subtitle = element_text(size = 9, hjust = 0.5, color = "grey30",
                                   lineheight = 1.4, margin = margin(b = 10)),
      plot.caption  = element_text(size = 8, hjust = 0, color = "grey40",
                                   lineheight = 1.5, margin = margin(t = 10)),
      plot.margin   = margin(15, 15, 15, 15)
    )
  )

fig2

suppressWarnings(
  ggsave("ggtree_derived_layouts.png", plot = fig2,
         width = 14, height = 16, dpi = 300, bg = "white")
)

# ============================================================
# FIGURE 3: Branch Styling (6 panels, 3x2)
# ============================================================

library(ltc)
alger <- ltc("alger", 6, "continuous")

# Use a smaller tree for readability with labels
set.seed(2017-02-16)
stree <- rtree(15)

s_a <- ggtree(stree) +
  ggtitle("A") + clean

s_b <- ggtree(stree, color = alger[1], linewidth = 1.2) +
  ggtitle("B") + clean

s_c <- ggtree(stree, color = alger[3], linetype = "dotted", linewidth = 1) +
  ggtitle("C") + clean

s_d <- ggtree(stree, color = alger[5], linewidth = 2) +
  ggtitle("D") + clean

s_e <- ggtree(stree, layout = "circular", color = alger[2], linewidth = 1) +
  ggtitle("E") + clean

s_f <- ggtree(stree, layout = "slanted", color = alger[6], linewidth = 1.5) +
  ggtitle("F") + clean

fig3 <- s_a + s_b + s_c +
  s_d + s_e + s_f +
  plot_layout(ncol = 3) +
  plot_annotation(
    title = "Branch Styling in ggtree",
    subtitle = paste0(
      "Customizing tree appearance with color, linewidth, and linetype."
    ),
    caption = paste(
      "(A) Default rectangular,",
      "(B) colored branches (alger[1]),",
      "(C) dotted branches (alger[3]),\n",
      "(D) thick branches (alger[5]),",
      "(E) circular colored (alger[2]),",
      "(F) slanted colored (alger[6])."
    ),
    theme = theme(
      plot.title    = element_text(size = 16, face = "bold", hjust = 0.5,
                                   margin = margin(b = 4)),
      plot.subtitle = element_text(size = 9, hjust = 0.5, color = "grey30",
                                   lineheight = 1.4, margin = margin(b = 10)),
      plot.caption  = element_text(size = 8, hjust = 0.5, color = "grey40",
                                   lineheight = 1.5, margin = margin(t = 10)),
      plot.margin   = margin(15, 15, 15, 15)
    )
  )

fig3
suppressWarnings(
  ggsave("ggtree_branch_styling.png", plot = fig3,
         width = 14, height = 10, dpi = 300, bg = "white")
)

# ============================================================
# FIGURE 4: Tips & Labels (6 panels, 3x2)
# ============================================================

t_a <- ggtree(stree) +
  geom_tippoint(color = alger[1], size = 3) +
  ggtitle("A") + clean

t_b <- ggtree(stree) +
  geom_point(aes(shape = isTip, color = isTip), size = 3) +
  scale_color_manual(values = c("TRUE" = alger[2], "FALSE" = alger[5])) +
  theme(legend.position = "none") +
  ggtitle("B") + clean

t_c <- ggtree(stree) +
  geom_nodepoint(color = alger[4], alpha = 0.4, size = 8) +
  geom_tippoint(color = alger[1], shape = 8, size = 3) +
  ggtitle("C") + clean

t_d <- ggtree(stree) +
  geom_tiplab(size = 3, color = alger[3]) +
  ggtitle("D") + clean

t_e <- ggtree(stree, layout = "circular") +
  geom_tiplab(aes(angle = angle), size = 3, color = alger[6]) +
  ggtitle("E") + clean

t_f <- ggtree(stree) +
  geom_tiplab(as_ylab = TRUE, color = alger[2]) +
  ggtitle("F") + clean

fig4 <- t_a + t_b + t_c +
  t_d + t_e + t_f +
  plot_layout(ncol = 3) +
  plot_annotation(
    title = "Tips & Labels in ggtree",
    subtitle = paste0(
      "Adding tip points, node points, and tip labels to trees."
    ),
    caption = paste(
      "(A) Tip points via geom_tippoint(),",
      "(B) tip vs node shape/color via geom_point(aes(isTip)),",
      "(C) node + tip points combined,\n",
      "(D) tip labels via geom_tiplab(),",
      "(E) circular tip labels with angle adjustment,",
      "(F) tip labels as y-axis via as_ylab = TRUE."
    ),
    theme = theme(
      plot.title    = element_text(size = 16, face = "bold", hjust = 0.5,
                                   margin = margin(b = 4)),
      plot.subtitle = element_text(size = 9, hjust = 0.5, color = "grey30",
                                   lineheight = 1.4, margin = margin(b = 10)),
      plot.caption  = element_text(size = 8, hjust = 0.5, color = "grey40",
                                   lineheight = 1.5, margin = margin(t = 10)),
      plot.margin   = margin(15, 15, 15, 15)
    )
  )

fig4

suppressWarnings(
  ggsave("ggtree_tips_labels.png", plot = fig4,
         width = 14, height = 10, dpi = 300, bg = "white")
)