ggtreeExtra

https://github.com/yulab-smu/ggtreeextra
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ggtreeExtra is an R package that extends methods for mapping and visualizing associated data on...
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### Install ggtreeExtra from GitHub

Source: https://github.com/yulab-smu/ggtreeextra/blob/master/README.md

Install the development version of ggtreeExtra from GitHub. Requires the devtools package.

```r
if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("xiangpin/ggtreeExtra")
```

--------------------------------

### Install ggtreeExtra from Bioconductor

Source: https://github.com/yulab-smu/ggtreeextra/blob/master/README.md

Install the released version of ggtreeExtra from Bioconductor. Ensure BiocManager is installed.

```r
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ggtreeExtra")
```

--------------------------------

### Install ggtreeExtra from Bioconductor and GitHub

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Installs the release version of ggtreeExtra from Bioconductor and the development version from GitHub. Ensure remotes and BiocManager are installed first.

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ggtreeExtra")
```

```r
if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("YuLab-SMU/ggtreeExtra")
```

--------------------------------

### Add Star Points Layer to Fan Tree with ggtreeExtra

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Demonstrates adding a layer of star plots to a fan-layout phylogenetic tree using geom_fruit. Requires loading tree and data, then applying geom_star with specific aesthetic mappings and scales.

```r
library(ggtreeExtra)
library(ggtree)
library(ggplot2)
library(ggstar)
library(ggnewscale)
library(treeio)

# Load bundled example data
trfile    <- system.file("extdata", "tree.nwk",              package = "ggtreeExtra")
tippoint  <- system.file("extdata", "tree_tippoint_bar.csv", package = "ggtreeExtra")
ring1file <- system.file("extdata", "first_ring_discrete.csv",  package = "ggtreeExtra")
ring2file <- system.file("extdata", "second_ring_continuous.csv", package = "ggtreeExtra")

tree <- read.tree(trfile)
dat1 <- read.csv(tippoint)   # columns: ID, Location, Length, Group, Abundance
dat2 <- read.csv(ring1file)  # columns: ID, Pos, Type
dat3 <- read.csv(ring2file)  # columns: ID, Type2, Alpha

# Base fan-layout tree
p <- ggtree(tree, layout = "fan", open.angle = 10, size = 0.5)

# Layer 1 – star points at tips (position="identity" keeps them on tip nodes)
p2 <- p +
    geom_fruit(
        data    = dat1,
        geom    = geom_star,
        mapping = aes(y = ID, fill = Location, size = Length, starshape = Group),
        position = "identity",
        starstroke = 0.2
    ) +
    scale_size_continuous(range = c(1, 3),
        guide = guide_legend(keywidth = 0.5, keyheight = 0.5,
                             override.aes = list(starshape = 15), order = 2)) +
    scale_fill_manual(
        values = c("#F8766D","#C49A00","#53B400","#00C094","#00B6EB","#A58AFF","#FB61D7"),
        guide  = "none") +
    scale_starshape_manual(values = c(1, 15),
        guide = guide_legend(keywidth = 0.5, keyheight = 0.5, order = 1),
        na.translate = FALSE)
```

--------------------------------

### Add Continuous Heatmap Ring with X-axis Annotation using ggtreeExtra

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Adds a continuous heatmap ring with alpha transparency and x-axis labels. This snippet demonstrates using geom_tile with new scale for fill and alpha, and configuring axis parameters for labels.

```r
p4 <- p3 +
    new_scale_fill() +
    geom_fruit(
        data    = dat3,
        geom    = geom_tile,
        mapping = aes(y = ID, x = Type2, alpha = Alpha, fill = Type2),
        pwidth  = 0.15,
        axis.params = list(
            axis       = "x",     # show x-axis labels
            text.angle = -45,
            hjust      = 0
        )
    ) +
    scale_fill_manual(
        values = c("#b22222","#005500","#0000be","#9f1f9f"),
        guide  = guide_legend(keywidth = 0.5, keyheight = 0.5, order = 4)) +
    scale_alpha_continuous(range = c(0, 0.4),
        guide = guide_legend(keywidth = 0.5, keyheight = 0.5, order = 5))
```

--------------------------------

### Bar Chart with position_dodgex

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Demonstrates using position_dodgex for standard and vertically/horizontally expanded dodging in bar charts. Useful for controlling spacing and alignment.

```R
p1 <- ggplot(iris, aes(x = Species, y = Petal.Length, fill = ID)) +
    geom_bar(stat = "identity", position = position_dodgex())
p2 <- ggplot(iris, aes(x = Species, y = Petal.Length, fill = ID)) +
    geom_bar(stat = "identity", position = position_dodgex(vexpand = 5))

p3 <- ggplot(iris, aes(x = Petal.Length, y = Species, fill = ID)) +
    geom_bar(stat = "identity", orientation = "y",
             position = position_dodgex(hexpand = 5))

p5 <- ggplot(iris, aes(x = Species, y = Petal.Length, fill = ID)) +
    geom_boxplot(position = position_dodgex2(vexpand = 5))

(p1 + p2 + p3) / p5
```

--------------------------------

### Combined Dodge and Jitter with position_jitterdodgex

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Illustrates using position_jitterdodgex to simultaneously dodge and jitter points, suitable for boxplots where points need to be spread within dodge groups. Requires a grouping aesthetic.

```R
library(ggplot2)
library(ggtreeExtra)

set.seed(123)
df <- data.frame(
    x     = rep(c("A","B","C"), each = 40),
    y     = rnorm(120),
    group = rep(c("g1","g2"), 60)
)

ggplot(df, aes(x = x, y = y, fill = group, color = group)) +
    geom_boxplot(position = position_dodgex(), outlier.shape = NA) +
    geom_point(shape = 21, size = 1.5,
               position = position_jitterdodgex(
                   jitter.width = 0.1,
                   dodge.width  = 0.75,
                   vexpand      = 0   # no global shift
               ))
```

--------------------------------

### Stack Multiple Geoms on Same Ring with geom_fruit_list

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Groups multiple geom_fruit layers and scales to render at the same radial position. Use when overlaying different geoms like bars and points that should share panel space.

```R
library(ggtreeExtra)
library(ggtree)
library(ggplot2)
library(ggstar)
library(ggnewscale)

set.seed(1024)
tr  <- rtree(100)
dt  <- data.frame(id = tr$tip.label, value = abs(rnorm(100)),
                  group  = c(rep("A", 50), rep("B", 50)))
df  <- dt; colnames(df)[3]  <- "group2"
dtf <- dt; colnames(dtf)[3] <- "group3"

# Base fan tree
p <- ggtree(tr, layout = "fan", open.angle = 0)

# Ring 1: simple bar chart
p1 <- p +
    geom_fruit(data = dt, geom = geom_col,
               mapping = aes(y = id, x = value, fill = group)) +
    new_scale_fill()

# Ring 2: bar + stars occupying the SAME outer ring via geom_fruit_list
p2 <- p1 +
    geom_fruit_list(
        geom_fruit(data = df, geom = geom_col,
                   mapping = aes(y = id, x = value, fill = group2)),
        scale_fill_manual(values = c("blue", "red")),
        new_scale_fill(),
        geom_fruit(data = dt, geom = geom_star,
                   mapping = aes(y = id, x = value, fill = group),
                   size = 2.5, color = NA, starstroke = 0)
    ) +
    new_scale_fill()

# Ring 3: another bar chart on its own ring
p3 <- p2 +
    geom_fruit(data = dtf, geom = geom_col,
               mapping = aes(y = id, x = value, fill = group3)) +
    scale_fill_manual(values = c("#00AED7", "#009E73"))
p3
```

--------------------------------

### Add Discrete Heatmap Ring with ggtreeExtra

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Adds a discrete heatmap ring as an external layer to a phylogenetic tree. Uses geom_tile and requires specifying offset and panel width relative to the tree's x-range.

```r
p3 <- p2 +
    new_scale_fill() +
    geom_fruit(
        data    = dat2,
        geom    = geom_tile,
        mapping = aes(y = ID, x = Pos, fill = Type),
        offset  = 0.08,   # gap between this ring and the previous layer
        pwidth  = 0.25    # ring width = 0.25 * x-range of tree
    ) +
    scale_fill_manual(values = c("#339933", "#dfac03"),
        guide = guide_legend(keywidth = 0.5, keyheight = 0.5, order = 3))
```

--------------------------------

### Jittered Points Overlaid on Boxplots with position_jitterx

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Shows how to overlay jittered points on boxplots using geom_fruit and position_jitterx. Requires setting a seed for reproducibility and ensures points are within their respective bands.

```R
library(ggtreeExtra)
library(ggtree)
library(ggplot2)

set.seed(1024)
tr  <- rtree(10)
df  <- data.frame(id = tr$tip.label, group = rep(c("A","B"), 5))
dat <- data.frame(id = rep(tr$tip.label, 8), value = rnorm(80, 0.5, 0.15))
dt  <- merge(dat, df, by = "id")

p <- ggtree(tr) %<+% df +
    geom_tiplab(align = TRUE, linesize = .1, size = 3)

# Boxplot layer
gf1 <- geom_fruit(data = dat, geom = geom_boxplot,
                  mapping = aes(x = value, y = id),
                  orientation = "y", offset = 0.1, pwidth = 0.9)

# Overlaid jittered points at the same x-range
set.seed(1024)
gf2 <- geom_fruit(data = dt, geom = geom_point,
                  mapping = aes(x = value, y = id, color = group),
                  offset = 0.1, pwidth = 0.9,
                  position = position_jitterx(height = 0.3),
                  axis.params = list(axis = "x", text.size = 2),
                  grid.params = list())

# Both layers share the same panel via geom_fruit_list
p + geom_fruit_list(gf1, gf2)
```

--------------------------------

### Identity Position with Global Shift using position_identityx

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Demonstrates position_identityx as a replacement for position_identity, allowing global horizontal (hexpand) or vertical (vexpand) shifts for geoms. Useful for precise layer alignment.

```R
library(ggplot2)
library(ggtreeExtra)
library(patchwork)

# Standard identity position
p1 <- ggplot(mtcars, aes(x = wt, y = mpg)) +
    geom_point(position = position_identityx()) +
    ylim(0, 50)

# Shift entire point layer up by 5 units
p2 <- ggplot(mtcars, aes(x = wt, y = mpg)) +
    geom_point(position = position_identityx(vexpand = 5)) +
    ylim(0, 50)

# Horizontal shift
p3 <- ggplot(mtcars, aes(y = wt, x = mpg)) +
    geom_point(position = position_identityx(hexpand = 5)) +
    xlim(0, 50)

p1 + p2 + p3
```

--------------------------------

### Sine-based Point Positioning for Ridgelines with position_points_sinax

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Positions points within ridgeline density bands using a sine distribution, controlled by rel_min/rel_max and hexpand for horizontal alignment. Ideal for overlaying points on density plots.

```R
library(ggplot2)
library(ggtreeExtra)
library(ggridges)  # for geom_density_ridges_gradient

set.seed(42)
df <- data.frame(
    species = sample(c("A","B","C"), 300, replace = TRUE),
    value   = rnorm(300)
)

ggplot(df, aes(x = value, y = species, fill = after_stat(x))) +
    geom_density_ridges_gradient(scale = 1.5) +
    geom_point(aes(x = value, y = species),
               position = position_points_sinax(
                   rel_min = 0.02,
                   rel_max = 0.98,
                   hexpand = 0
               ),
               size = 0.8, alpha = 0.4) +
    scale_fill_viridis_c()
```

--------------------------------

### Pipe-Friendly Alias for geom_fruit() with fruit_plot()

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Uses fruit_plot, a convenience alias for geom_fruit, which accepts the tree plot as the first argument, making it suitable for magrittr pipe chains.

```R
library(ggtreeExtra)
library(ggtree)
library(ggplot2)
library(magrittr)

set.seed(42)
tr <- rtree(50)
dd <- data.frame(id = tr$tip.label, score = abs(rnorm(50)))

ggtree(tr, layout = "circular") %>%
    fruit_plot(
        data    = dd,
        geom    = geom_col,
        mapping = aes(y = id, x = score),
        pwidth  = 0.3,
        offset  = 0.05
    )
```

--------------------------------

### Stack Bar Charts with Optional Global Shift using position_stackx

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Extends ggplot2::position_stack with hexpand and vexpand for shifting stacked layers. This is the default position for geom_bar and geom_col in geom_fruit.

```R
library(ggplot2)
library(ggtreeExtra)

df <- data.frame(trt = c("a","b","c"), outcome = c(2.3, 1.9, 3.2))

# Standard stack
p1 <- ggplot(df, aes(x = trt, y = outcome)) +
    geom_bar(stat = "identity", position = position_stackx())

# Shift entire stacked layer up by 5 units on the y-axis
p2 <- ggplot(df, aes(x = trt, y = outcome)) +
    geom_bar(stat = "identity", position = position_stackx(vexpand = 5))

# Horizontal orientation with horizontal shift
p3 <- ggplot(df, aes(x = outcome, y = trt)) +
    geom_bar(stat = "identity", orientation = "y",
             position = position_stackx(hexpand = 5))

library(patchwork)
p1 + p2 + p3
```

--------------------------------

### Add Bar Chart with Grid Lines to Tree

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Adds a bar chart layer with custom fill colors and legend options to a tree plot. Grid lines are enabled by default.

```R
p5 <- p4 +
    new_scale_fill() +
    geom_fruit(
        data    = dat1,
        geom    = geom_col,
        mapping = aes(y = ID, x = Abundance, fill = Location),
        pwidth  = 0.4,
        axis.params = list(axis = "x", text.angle = -45, hjust = 0),
        grid.params = list()  # default grey grid lines
    ) +
    scale_fill_manual(
        values = c("#F8766D","#C49A00","#53B400","#00C094","#00B6EB","#A58AFF","#FB61D7"),
        guide  = guide_legend(keywidth = 0.5, keyheight = 0.5, order = 6))
    theme(legend.background = element_rect(fill = NA),
          legend.title = element_text(size = 7),
          legend.text  = element_text(size = 6),
          legend.spacing.y = unit(0.02, "cm"))
p5
```

--------------------------------

### Dodge Geoms with Optional Global Shift using position_dodgex

Source: https://context7.com/yulab-smu/ggtreeextra/llms.txt

Extends ggplot2::position_dodge and position_dodge2 with hexpand/vexpand offsets. These are the default positions for geom_violin and geom_boxplot in geom_fruit.

```R
library(ggplot2)
library(ggtreeExtra)
library(patchwork)

iris$ID <- rep(c(rep("test1",15), rep("test2",15), rep("test3",20)), 3)


```
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