Stack Layout

stack_layout() arranges plots either horizontally or vertically, and can be referred to using the alias ggstack(). There are two types of stack layouts:

stack_align(): align the observations along the stack.
stack_free(): don’t align the observations.

Several aliases are available for convenience:

stack_alignv: Aligns the stack vertically (special case of stack_align()).
stack_alignh: Aligns the stack horizontally (special case of stack_align()).
stack_freev: A vertical version of stack_free().
stack_freeh: A horizontal version of stack_free(). direction = "horizontal".

library(ggalign)
#> Loading required package: ggplot2

Input data

For stack_free(), a data frame is required, and the input will be automatically converted using fortify_data_frame() if needed.
For stack_align(), a matrix is required, and the input will be automatically converted using fortify_matrix() if needed.

set.seed(123)
small_mat <- matrix(rnorm(56), nrow = 7)
rownames(small_mat) <- paste0("row", seq_len(nrow(small_mat)))
colnames(small_mat) <- paste0("column", seq_len(ncol(small_mat)))

By default, stack_align()/stack_free() will set up the layout, but no plot will be drawn until you add a plot element:

stack_alignh(small_mat)

# stack_freev(small_mat) # the same for `stack_free()`

plot element

For stack_align(), plots can be added regardless of whether they need to align observations.

stack_alignh(small_mat) + align_dendro()

stack_alignh(small_mat) +
    align_kmeans(centers = 3L) +
    ggalign(data = rowSums) +
    geom_bar(aes(value, fill = .panel), orientation = "y", stat = "identity") +
    facet_grid(switch = "y") +
    theme(strip.text = element_text()) +
    align_dendro(aes(color = branch))

We can stack the plots vertically with stack_alignv():

stack_alignv(small_mat) + align_dendro()

Note that vertical stack take the x-axis as the observations, but horizontal stack take the y-axis as the observations.

stack_align() can add plot without alignment of observations.

stack_alignv() +
    ggfree(aes(displ, hwy, colour = class), data = mpg) +
    geom_point(size = 2) +
    ggfree(aes(displ, hwy, colour = class), data = mpg) +
    geom_point(size = 2) &
    scale_color_brewer(palette = "Dark2") &
    theme_bw()

For stack_free(), only plots that are free from alignment (ggfree()) can be added along the axis. stack_free() alone is not very useful, since we can combine multiple plots vertically or horizontally with align_plots() or patchwork. The only benefits would be the data can be inherited by multiple plots.

stack_freev(mpg) +
    ggfree(aes(displ, hwy, colour = class)) +
    geom_point(size = 2) +
    ggfree(aes(displ, hwy, colour = class)) +
    geom_point(size = 2) &
    scale_color_brewer(palette = "Dark2") &
    theme_bw()

`ggheatmap()`/`quad_layout()`

ggheatmap()/quad_layout() can be added to a stack layout.

stack_alignh(small_mat) +
    ggheatmap()
#> → heatmap built with `geom_tile()`

However, as noted earlier, stack_free() can only accept plots that are free from alignment along the axis. Here’s a table summarizing which layouts are compatible with stack_free():

	`stack_freeh()`	`stack_freev()`
`quad_free()`/`ggside()`	✅	✅
`quad_alignh()`	❌	✅
`quad_alignv()`	✅	❌
`quad_alignb()`/`ggheatmap()`	❌	❌

alignh_quad_plot <- quad_alignh(small_mat) +
    geom_boxplot(aes(value, .row_names, fill = .row_names)) +
    scale_fill_brewer(palette = "Dark2")
stack_freev() +
    alignh_quad_plot +
    alignh_quad_plot

The data of ggheatmap()/quad_layout() can inherit from the parent stack_layout(), but the data format must match. Otherwise, you will need to manually provide the data. When ggheatmap()/quad_layout() is added to a vertical stack_align(), the inherited matrix is transposed before use.

stack_alignv(small_mat) +
    ggheatmap()
#> → heatmap built with `geom_tile()`

Once a ggheatmap()/quad_layout() is added, any further elements you add will be applied to this ggheatmap()/quad_layout(). You can include align_* elements or any ggplot2 components for the quad_layout().

stack_alignh(small_mat) +
    ggheatmap()
#> → heatmap built with `geom_tile()`

If you’d like to add elements to the stack layout rather than the ggheatmap()/quad_layout() layout, you can easily switch from the ggheatmap()/quad_layout() to the stack layout using stack_active().

stack_alignh(small_mat) +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0)) +
    stack_active() +
    ggalign(data = rowSums) +
    geom_bar(aes(value), fill = "red", orientation = "y", stat = "identity")
#> → heatmap built with `geom_tile()`

One exception is the ggheatmap()/quad_layout() itself, which cannot be added to another heatmap layout. Therefore, you can directly add a ggheatmap()/quad_layout() to the stack layout without using stack_active().

stack_alignv(small_mat) +
    ggheatmap() +
    ggheatmap()
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`

Control sizes

A length of 3 sizes should be provided in stack_align()/stack_free() when putting a heatmap with flank annotation into the stack layout. For vertical stacks, this means heatmaps with left or right annotations; for horizontal stacks, this means heatmaps with top or bottom annotations. The first size controls the relative width/height of the left or top annotation, the second controls the relative size of the heatmap body width/height, and the third controls the relative width/height of the right or bottom annotation.

By default the three rows/columns will have equal sizes.

stack_alignv(small_mat) +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0)) +
    anno_left() +
    align_dendro(aes(color = .panel), k = 3L) +
    anno_right() +
    ggalign(data = rowSums) +
    geom_bar(aes(value, fill = .panel), orientation = "y", stat = "identity") +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0))
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`

# the left annotation, will have a relative size 1
# the heatmap body will have a relative width 2
# the right annotation will have a relative size 1
stack_alignv(small_mat, sizes = c(1, 2, 1)) +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0)) +
    anno_left() +
    align_dendro(aes(color = .panel), k = 3L) +
    anno_right() +
    ggalign(data = rowSums) +
    geom_bar(aes(value, fill = .panel), orientation = "y", stat = "identity") +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0))
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`

In this way, heatmap body width/height specified in quad_active() or ggheatmap() won’t work.

stack_alignv(small_mat) +
    ggheatmap(width = unit(2, "null")) + # not work
    theme(axis.text.x = element_text(angle = -60, hjust = 0)) +
    anno_left() +
    align_dendro(aes(color = .panel), k = 3L) +
    anno_right() +
    ggalign(data = rowSums) +
    geom_bar(aes(value, fill = .panel), orientation = "y", stat = "identity") +
    ggheatmap(width = unit(2, "null")) + # not work
    theme(axis.text.x = element_text(angle = -60, hjust = 0))
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`

By default the flank annotation will fill the whole stack flank, but we can still control the size of heatmap annotation in quad_anno().

stack_alignv(small_mat) +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0)) +
    # the left annotation will have a total size 2cm
    anno_left(size = unit(2, "cm")) +
    align_dendro(aes(color = .panel), k = 3L) +
    anno_right() +
    ggalign(data = rowSums) +
    geom_bar(aes(value, fill = .panel), orientation = "y", stat = "identity") +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0))
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`

You can also use npc unit.

stack_alignv(small_mat) +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0)) +
    # the left annotation will have a total width 1/2 npc
    anno_left(size = unit(0.5, "npc")) +
    align_dendro(aes(color = .panel), k = 3L) +
    anno_right() +
    ggalign(data = rowSums) +
    geom_bar(aes(value, fill = .panel), orientation = "y", stat = "identity") +
    ggheatmap() +
    theme(axis.text.x = element_text(angle = -60, hjust = 0))
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`

Session information

sessionInfo()
#> R version 4.4.2 (2024-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.5 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] ggalign_0.0.5.9000 ggplot2_3.5.1     
#> 
#> loaded via a namespace (and not attached):
#>  [1] gtable_0.3.6       jsonlite_1.8.9     dplyr_1.1.4        compiler_4.4.2    
#>  [5] tidyselect_1.2.1   jquerylib_0.1.4    systemfonts_1.1.0  scales_1.3.0      
#>  [9] textshaping_0.4.0  yaml_2.3.10        fastmap_1.2.0      R6_2.5.1          
#> [13] labeling_0.4.3     generics_0.1.3     knitr_1.49         tibble_3.2.1      
#> [17] desc_1.4.3         munsell_0.5.1      bslib_0.8.0        pillar_1.9.0      
#> [21] RColorBrewer_1.1-3 rlang_1.1.4        utf8_1.2.4         cachem_1.1.0      
#> [25] xfun_0.49          fs_1.6.5           sass_0.4.9         cli_3.6.3         
#> [29] pkgdown_2.1.1      withr_3.0.2        magrittr_2.0.3     digest_0.6.37     
#> [33] grid_4.4.2         lifecycle_1.0.4    vctrs_0.6.5        evaluate_1.0.1    
#> [37] glue_1.8.0         farver_2.1.2       ragg_1.3.3         fansi_1.0.6       
#> [41] colorspace_2.1-1   rmarkdown_2.29     tools_4.4.2        pkgconfig_2.0.3   
#> [45] htmltools_0.5.8.1

Input data

plot element

ggheatmap()/quad_layout()

Control sizes

Session information

`ggheatmap()`/`quad_layout()`