Sorry, the internal will build a patchwork firstly, but plotly doesn't support the patchwork. So it's not possible for this to work with ggplotly. Please see https://github.com/plotly/plotly.R/issues/2028 for details

Yes, it internally use facet to plot the heatmap groups. The dendrogram will be aligned well with any ggplot objects (Just use the ggalign function to create a ggplot plot) in the facet layout.

I have changed the default theme, and it can support connect multiple heatmap horizontally or vertically.

Because it can now align a dendrogram in a standard ggplot2 plot, enhancing its versatility, and it has been renamed into ggalign:

mat <- matrix(rnorm(81), nrow = 9)
rownames(mat) <- paste0("row", seq_len(nrow(mat)))
colnames(mat) <- paste0("column", seq_len(ncol(mat)))
ggheatmap(mat) +
  scale_fill_viridis_c() +
  hmanno("t") +
  align_dendro(aes(color = branch), k = 3L) +
  ggalign(aes(y = value), data = rowSums) +
  geom_bar(stat = "identity", aes(fill = factor(.panel))) +
  scale_fill_brewer(name = NULL, palette = "Dark2") +
  hmanno("l") +
  ggalign(aes(x = value), data = rowSums, size = 0.5) +
  geom_bar(
    aes(y = .y, fill = factor(.y)),
    stat = "identity",
    orientation = "y"
  ) +
  scale_x_reverse() +
  align_dendro(aes(color = branch),
    size = unit(1, "null"),
    k = 4L
  ) +
  scale_x_reverse()

^{Created on 2024-07-17 with [reprex v2.1.0](https://reprex.tidyverse.org)} ~

layout_stack put plots horizontally or vertically. You can also use the alias ggstack.

set.seed(123)
mat1 <- matrix(rnorm(80, 2), 8, 10)
mat1 <- rbind(mat1, matrix(rnorm(40, -2), 4, 10))
rownames(mat1) <- paste0("R", 1:12)
colnames(mat1) <- paste0("C", 1:10)

mat2 <- matrix(runif(60, max = 3, min = 1), 6, 10)
mat2 <- rbind(mat2, matrix(runif(60, max = 2, min = 0), 6, 10))
rownames(mat2) <- paste0("R", 1:12)
colnames(mat2) <- paste0("C", 1:10)

le <- sample(letters[1:3], 12, replace = TRUE)
names(le) <- paste0("R", 1:12)

ind <- sample(12, 12)
mat1 <- mat1[ind, ]
mat2 <- mat2[ind, ]
le <- le[ind]
ht1 <- ggheatmap(mat1, width = 1) +
  scale_fill_viridis_c() +
  hmanno("t") +
  align_dendro(k = 3L) +
  scale_y_continuous(expand = expansion()) +
  hmanno(NULL)
ht2 <- ggheatmap(mat2, width = 1)
ggstack(mat1, rel_sizes = c(0.2, 1, 1)) +
  align_dendro(size = 0.2) +
  scale_x_reverse() +
  ht1 +
  ht2 +
  ggalign(data = le, size = 0.2) +
  geom_tile(aes(x = .column_index, fill = value)) +
  scale_x_continuous(name = NULL, labels = NULL, breaks = NULL) &
  theme(plot.margin = margin())