Layout Plots

The ggalign package offers several align_* functions that allow for precise control over plot layouts. In addition, there are two primary functions for adding plots:

align_gg()/ggalign(): Create a ggplot object and aligns the observation data.
free_gg()/ggfree(): Create a ggplot object without aligning the observation data.

align_gg()/ggalign() can only be used with a stack_layout() that aligns observations (stack_align()), while free_gg()/ggfree() can also be added to a stack_layout() that does not align the observations (stack_free()).

library(ggalign)
#> Loading required package: ggplot2

set.seed(123)
small_mat <- matrix(rnorm(81), nrow = 9)
rownames(small_mat) <- paste0("row", seq_len(nrow(small_mat)))
colnames(small_mat) <- paste0("column", seq_len(ncol(small_mat)))

`align_gg`/`ggalign`

align_gg() is similar to ggplot in that it initializes a ggplot data and mapping. Same with other align_* functions. align_gg() allowing you to provide data in various formats, including matrices, data frames, or simple vectors. By default, it will inherit from the layout. If a function, it will apply with the layout matrix.

align_gg() always applies a default mapping for the axis of the data index in the layout. This mapping is aes(y = .data$.y) for horizontal stacking (including left and right quad layout annotation) and aes(x = .data$.x) for vertical stacking (including top and bottom quad layout annotation). For more information, refer to the “ggplot2 Specification” section in the align_gg() documentation.

You can also use the ggalign() function, which is an alias for align_gg().

The data in the underlying ggplot object will contain following columns:

.panel: the panel for the aligned axis. It means x-axis for vertical stack layout (including top and bottom annotation), y-axis for horizontal stack layout (including left and right annotation).
.x or .y: the x or y coordinates.
.names and .index: A factor of the names (only applicable when names exists) and an integer of index of the original data.
.row_names and .row_index: the row names and an integer of row index of the original matrix (only applicable if data is a matrix).
.column_names and .column_index: the column names and column index of the original matrix (only applicable if data is a matrix).
value: the actual value (only applicable if data is a matrix or atomic vector).

It is recommended to use .x/.y, or .names as the x/y mapping.

ggheatmap(small_mat) +
    scale_fill_viridis_c(guide = "none") +
    anno_top() +
    ggalign(data = rowSums) +
    geom_point(aes(y = value))
#> → heatmap built with `geom_tile()`

If data = NULL, the data in the underlying ggplot object contains following columns:

.panel: the panel for the axis used for alignment.
.index: the index of the original layout data.
.x or .y: the x or y coordinates

You can use it to integrate additional elements, such as block annotation or customized panel title, into your layout.

ggheatmap(small_mat) +
    anno_top(size = unit(1, "cm")) +
    align_kmeans(centers = 3L) +
    ggalign(data = NULL) +
    plot_data(~ aggregate(.x ~ .panel, .x, FUN = median)) +
    geom_tile(aes(y = 1L, fill = .panel, color = .panel)) +
    geom_text(aes(y = 1L, label = .panel))
#> → heatmap built with `geom_tile()`

Cross panel sumamry

When used in a ggheatmap(), and the data is inherited from the ggheatmap(), a special column .extra_panel will be added, which is the panel information for column (left or right annotation) or row (top or bottom annotation). This is useful if you want to create summary plot using another axis panel. In such cases, it’s often necessary to disable the automatic setting of limits (limits = FALSE in ggalign()).

set.seed(1L)
v <- stats::rnorm(50L)
split <- sample(letters[1:2], 50L, replace = TRUE)
ggheatmap(v) +
    theme(strip.text = element_text(), strip.background = element_rect()) +
    anno_right() +
    align_group(split) +
    anno_top(size = 0.5) +
    ggalign(limits = FALSE) +
    geom_boxplot(aes(.extra_panel, value, fill = .extra_panel),
        # here, we use `print()` to show the underlying data
        data = function(data) {
            print(head(data))
            data
        }
    ) +
    scale_fill_brewer(palette = "Dark2", name = "branch")
#> → heatmap built with `geom_tile()`

#>   .row_index .column_index      value .index .panel .x .extra_panel
#> 1          1             1 -0.6264538      1      1  1            b
#> 2          1             2  0.1836433      1      1  1            b
#> 3          1             3 -0.8356286      1      1  1            b
#> 4          1             4  1.5952808      1      1  1            a
#> 5          1             5  0.3295078      1      1  1            a
#> 6          1             6 -0.8204684      1      1  1            a

This approach replicates the functionality of ComplexHeatmap::anno_summary(), but is versatile enough to be used with any heatmap, not just single-column or single-row heatmaps.

ggheatmap(small_mat) +
    theme(axis.text.x = element_text(angle = -60, hjust = 0)) +
    anno_top() +
    align_dendro(aes(color = branch), k = 3L) +
    scale_color_brewer(palette = "Dark2") +
    anno_right(size = 0.5) +
    ggalign(limits = FALSE) +
    geom_boxplot(aes(y = .extra_panel, x = value, fill = factor(.extra_panel))) +
    scale_fill_brewer(palette = "Dark2", name = "branch")
#> → heatmap built with `geom_tile()`

Plot titles

ggplot2 only allow add titles in the top or add caption in the bottom. The ggalign package extends this capability, allowing you to place titles around any border of the plot using the patch_titles() function.

ggheatmap(small_mat) +
    patch_titles(left = "left patch title", bottom = "bottom patch title") +
    theme(axis.text.x = element_text(angle = -60, hjust = 0)) +
    anno_top() +
    align_dendro(aes(color = branch), k = 3L) +
    scale_color_brewer(palette = "Dark2") +
    patch_titles(top = "top patch title") +
    anno_right(size = 0.5) +
    ggalign(limits = FALSE) +
    geom_boxplot(aes(y = .extra_panel, x = value, fill = factor(.extra_panel))) +
    scale_fill_brewer(palette = "Dark2", name = "branch") +
    patch_titles(right = "right patch title")
#> → heatmap built with `geom_tile()`

`free_gg`/`ggfree`

The free_gg() function allows you to incorporate a ggplot object into your layout. Unlike align_gg(), which aligns every axis value precisely, free_gg() focuses on layout integration without enforcing strict axis alignment. ggfree() is an alias for free_gg.

Internally, the function uses fortify_data_frame() to transform the input into a data frame. For matrices, it converts them into a long-formatted data frame. Note that ggfree() does not provide a default aesthetic mapping, which contrasts with ggalign(). You will need to manually provide the default mappings.

All annotations in ggheatmap() are stack_align(). When used in a stack_align(), you typically do not want to inherit from the layout matrix and should input a data frame manually. The data argument must be explicitly provided, as it comes after ..., but we rarely used it in a stack_align().

ggheatmap(small_mat) +
    anno_top() +
    ggfree(aes(wt, mpg), data = mtcars) +
    geom_point()
#> → heatmap built with `geom_tile()`

It is more commonly used in a stack_free(), where you usually want to inherit from the layout data frame. All annotations in ggside() are stack_free().

ggside(mpg, aes(displ, hwy, colour = class)) -
    geom_point(size = 2) +
    anno_top(size = 0.3) +
    ggfree() +
    geom_density(aes(displ, y = after_stat(density), colour = class), position = "stack") +
    anno_right(size = 0.3) +
    ggfree() +
    geom_density(aes(x = after_stat(density), hwy, colour = class),
        position = "stack"
    ) +
    theme(axis.text.x = element_text(angle = 90, vjust = .5))

Alternatively, you can directly input the ggplot object.

ggheatmap(small_mat) +
    anno_top() +
    ggfree(data = ggplot(mtcars, aes(wt, mpg))) +
    geom_point()
#> → heatmap built with `geom_tile()`

You can also add the ggplot object directly without using ggfree(). However, doing so will limit control over the plot (like plot area size, and active components):

ggheatmap(small_mat) +
    anno_top() +
    ggplot(mtcars, aes(wt, mpg)) +
    geom_point()
#> → heatmap built with `geom_tile()`

`ggwrap()` and `inset()`

The ggwrap() function allows you to wrap objects that can be converted into a grob, turning them into a ggplot for plotting. Further you can still add ggplot elements like title, subtitle, tag, caption, and geoms using the same approach as with normal ggplots (using ggtitle(), labs(), geom_*()) as well as styling using theme(). This enables you to pass these wrapped objects into ggfree().

library(grid)
ggheatmap(small_mat) +
    anno_top() +
    # `ggwrap()` will create a `ggplot` object, we use `ggfree` to add it into the layout
    ggfree(data = ggwrap(rectGrob(gp = gpar(fill = "goldenrod")), align = "full"))
#> → heatmap built with `geom_tile()`

You can also integrate base plots, pheatmap, ComplexHeatmap, e.g.

Additionally, you can add any graphics as a inset to a ggplot using the inset() function. Like ggwrap(), inset() can accept any object that can be converted to a grob.

ggheatmap(small_mat) +
    anno_top() +
    ggfree(data = ggwrap(rectGrob(gp = gpar(fill = "goldenrod")), align = "full")) +
    # we can then add any inset grobs (the same as ggwrap, it can take any objects
    # which can be converted to a `grob`)
    inset(rectGrob(gp = gpar(fill = "steelblue")), align = "panel") +
    inset(textGrob("Here are some text", gp = gpar(color = "black")),
        align = "panel"
    )
#> → 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] grid      stats     graphics  grDevices utils     datasets  methods  
#> [8] 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      RColorBrewer_1.1-3 bslib_0.8.0       
#> [21] pillar_1.9.0       rlang_1.1.4        utf8_1.2.4         cachem_1.1.0      
#> [25] xfun_0.49          fs_1.6.5           sass_0.4.9         viridisLite_0.4.2 
#> [29] cli_3.6.3          pkgdown_2.1.1      withr_3.0.2        magrittr_2.0.3    
#> [33] digest_0.6.37      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

align_gg/ggalign