Align a dendrogram with faceted time series

Question

I am doing some time series clustering, and would like to align the dendrogram with the time series shapes. This is almost there:

library(ggplot2)
library(reshape2)
library(stats)
library(patchwork)
library(ggdendro) # Added ggdendro library

# ---- Example data: 4 time series ----
set.seed(1)
time <- 1:50
data <- data.frame(
  time = time,
  A = cumsum(rnorm(50, 0, 1)),
  B = cumsum(rnorm(50, 0, 1)),
  C = cumsum(rnorm(50, 0.2, 1)),
  D = cumsum(rnorm(50, -0.2, 1))
)

# Melt to long format for ggplot
df_long <- melt(data, id.vars = "time", variable.name = "series", value.name = "value")

# ---- Dendrogram (right panel) ----
# Compute hierarchical clustering on series
mat <- t(as.matrix(data[ , -1]))  # series as rows
d <- dist(mat)
hc <- hclust(d)

# Convert dendrogram to a ggplot-friendly format and adjust orientation
# We'll create the dendrogram first so we can order the time series plots accordingly
dendro_plot <- ggdendrogram(hc, rotate = TRUE, theme_dendro = FALSE) +
  scale_x_reverse() + # Reverse the x-axis to put leaves on the left
  theme_minimal() +
  theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(), # Remove y-axis labels and ticks on dendrogram
        plot.margin = margin(t = 0, r = 0, b = 0, l = 0)) # Adjust margins

# Reorder the data based on dendrogram order
ordered_series <- hc$labels[hc$order]
df_long$series <- factor(df_long$series, levels = ordered_series, ordered = TRUE)

# ---- Time series plots (left panel) ----
# Create a single ggplot object with facets for each series, ordered by the dendrogram
time_series_plot <- ggplot(df_long, aes(x = time, y = value)) +
  geom_line(linewidth = 1) +
  geom_hline(yintercept = 0, linetype="dashed") + 
  facet_grid(series ~ ., switch = "y") + # Facet by series with free y-scales and y-axis on the left
  theme_minimal() +
  labs(x = "Time", y = "Value") +
  theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(), # Remove y-axis labels and ticks on individual facets
        axis.title.y = element_blank(), # Remove overall y-axis title
        strip.text.y.left = element_text(angle = 0), # Orient facet labels horizontally on the left
        panel.spacing.y = unit(0.1, "lines"), # Reduce space between facets
        plot.margin = margin(t = 0, r = 0, b = 0, l = 0)) # Adjust margins


# ---- Combine ----
time_series_plot + dendro_plot + plot_layout(widths = c(3, 1), heights = unit(1,"null")) # Use heights = unit(1,"null") to make them proportional

Is there some easier way to do this that I'm just missing?

cuttlefish44 · Accepted Answer · 2025-10-31 07:15:30Z

The height of facet_grid panels are the same. So if you set panel.spacing.y = uint(0) at timeseries plot and set scale_x_continuous(limits = c(0.5, n_distinct(df_long$series) + 0.5), expand = 0) at dendrogram, 1:n_distinct(df_long$series) are just align with center of left panels.

(And I feel that panel.spacing.y = unit(0.1, "lines") has no practical problem when in use. )

dendro_plot <- ggdendrogram(hc, rotate = TRUE, heme_dendro = FALSE) +
  theme_minimal() +
  scale_x_reverse() + 
  scale_x_continuous(limits = c(0.5, n_distinct(df_long$series) + 0.5), expand = 0) +  # !! CORE CODE !!
  theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(), # Remove y-axis labels and ticks on dendrogram
        plot.margin = margin(t = 0, r = 0, b = 0, l = 0))  # Adjust margins


# ---- Time series plots (left panel) ----
# Create a single ggplot object with facets for each series, ordered by the dendrogram
time_series_plot <- ggplot(df_long, aes(x = time, y = value)) +
  geom_line(linewidth = 1) +
  geom_hline(yintercept = 0, linetype="dashed") + 
  # facet_grid(series ~ ., switch = "y") + # Facet by series with free y-scales and y-axis on the left
  facet_grid(series ~ .) +  # just check
  theme_minimal() +
  labs(x = "Time", y = "Value") +
  theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(), # Remove y-axis labels and ticks on individual facets
        axis.title.y = element_blank(), # Remove overall y-axis title
        strip.text.y.left = element_text(angle = 0), # Orient facet labels horizontally on the left
        panel.spacing.y = unit(0.1, "lines"), # Reduce space between facets
        plot.margin = margin(t = 0, r = 0, b = 0, l = 0)) # Adjust margins

# ---- Combine ----
time_series_plot + dendro_plot + plot_layout(widths = c(3, 1), heights = unit(1,"null")) # Use heights = unit(1,"null") to make them proportional

miken32 · Accepted Answer · 2025-11-04 00:14:00Z

-1

It's easy to create such plots using ggalign, which offers an integrative, composable visualization framework for ggplot2..


library(ggalign)
set.seed(1)
time <- 1:50
data <- t(data.frame(
    A = cumsum(rnorm(50, 0, 1)),
    B = cumsum(rnorm(50, 0, 1)),
    C = cumsum(rnorm(50, 0.2, 1)),
    D = cumsum(rnorm(50, -0.2, 1))
))

stack_discreteh(data) -
    # set default theme for all plots in the layout
    scheme_theme(theme_minimal()) +

    # add line plot
    ggfree(size = 3) +
    scheme_data(function(d) {
        d$time <- time[d$.column_index]
        d$.panel <- factor(d$.panel)
        names(d$.panel)
        d
    }) +
    geom_line(aes(time, value)) +
    geom_hline(yintercept = 0, linetype = "dashed") +
    facet_grid(rows = vars(.panel)) +
    theme(strip.text = element_blank(), strip.background = element_blank()) +

    # add the dendrogram
    align_dendro(aes(color = branch), k = 4, plot_cut_height = FALSE) +
    scale_color_brewer(palette = "Dark2", guide = "none") +
    theme(axis.text.y = element_text())

edited Nov 4 at 0:14

miken32

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answered Nov 3 at 17:50

Yun

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miken32 Nov 4 at 0:14

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