Difference with ggplot2

ggalign focuses on aligning observations across multiple plots. While it builds on the ggplot2 framework, there are key differences in how scales, facets, and coordinates are handled in alignment axes. This vignette highlights these syntax differences.

The following syntax applies to all align_* functions that add a plot area, and to the main plot in quad_layout() when alignment is needed.

Axes used for alignment

Axes used for alignment in ggalign refer to: - x-axis in vertical stack layouts

x-axis in horizontal stack layouts
x- and y axes in the quad_layout() main plot

ggalign introduces special syntax and handling for these axes, differing from the default behavior in ggplot2. These adjustments ensure that observations are properly aligned and operations are user-friendly.

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)))

Position Scales

To better fit the alignment-based layout, ggalign introduces adjustments to breaks, labels, and expand arguments.

breaks

breaks and labels are typically handled similarly to discrete scales, as we focus on aligning observations (which should be regarded as discrete variables) in the layout axis; however, a continuous scale can remain be used.

breaks should be one of:

- `NULL` for no breaks

- `waiver()` for the default breaks (the full data index or `NULL` if no
data names and `labels` is `waiver()`)

- A character vector of breaks (rownames / colunames of the matrix).

- A numeric vector of data index (must be an integer).

- A function that takes the data limits or the data index as input and
returns breaks as output. Also accepts rlang lambda function notation.

ggheatmap(small_mat) + scale_x_continuous(breaks = NULL)
#> → heatmap built with `geom_tile()`

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

no_names <- small_mat
colnames(no_names) <- NULL
ggheatmap(no_names) + scale_x_continuous()
#> → heatmap built with `geom_tile()`

ggheatmap(small_mat) + scale_x_continuous(breaks = c("column3", "column5"))
#> → heatmap built with `geom_tile()`

ggheatmap(small_mat) + scale_x_continuous(breaks = c(3, 5))
#> → heatmap built with `geom_tile()`

Floating number were not allowed in breaks.

ggheatmap(small_mat) + scale_x_continuous(breaks = c(3.5, 5))
#> → heatmap built with `geom_tile()`
#> Error in `scale_x_continuous()`:
#> ! Can't convert from `breaks` <double> to <integer> due to loss of precision.
#> • Locations: 1

labels

labels should be one of:

- `NULL` for no labels

- `waiver()` for the default labels (data names)

- A character vector giving labels (must be same length as breaks)

- An expression vector (must be the same length as breaks). See `?plotmath`
for details. 

- A function that takes the data names (or breaks if data has no names) as
input and returns labels as output. This can be also a rlang lambda
function.

ggheatmap(small_mat) + scale_x_continuous(labels = NULL)
#> → heatmap built with `geom_tile()`

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

ggheatmap(small_mat) +
    scale_x_continuous(labels = letters[seq_len(ncol(small_mat))])
#> → heatmap built with `geom_tile()`

ggheatmap(small_mat) +
    scale_x_continuous(breaks = c(3, 5), labels = c("a", "b"))
#> → heatmap built with `geom_tile()`

data ordering

Both breaks and labels should be provided in the original order of the raw data, the internal will reorder them accordingly if you reorder the observations.

index <- order(colMeans(small_mat))
xlabels <- letters[seq_len(ncol(small_mat))]
print(xlabels[index])
#> [1] "c" "h" "i" "g" "f" "e" "a" "b" "d"

ggheatmap(small_mat) +
    scale_x_continuous(labels = xlabels) +
    anno_top() +
    align_order(index)
#> → heatmap built with `geom_tile()`

expand

By default, we utilize zero expansion for the aligned axis. This is typically the desired setting. If you wish to introduce expansion, you must manually adjust it and apply it to each plot to ensure proper axis alignment.

ggheatmap(small_mat) +
    scale_x_continuous(expand = expansion(mult = 0.1)) +
    anno_top() +
    align_dendro(aes(color = branch), k = 3L) +
    scale_x_continuous(expand = expansion(mult = 0.1))
#> → heatmap built with `geom_tile()`

theme

Although ggplot2 does not officially support vectorized input for theme elements, we can still utilize it. For layout axis theme elements such as axis.text, axis.ticks, and axis.ticks.length, these will be reordered according to the layout axis ordering.

ggheatmap(small_mat) +
    theme(
        axis.text.x = element_text(
            colour = c(rep("red", 4), rep("blue", 5))
        ),
        axis.ticks.x = element_line(
            colour = c(rep("red", 4), rep("blue", 5))
        ),
        axis.ticks.length.x = unit(rep(c(1, 4), times = c(4, 5)), "mm")
    ) +
    anno_top() +
    align_dendro(aes(color = branch), k = 3L) +
    scale_y_continuous(expand = expansion()) &
    theme(plot.margin = margin())
#> Warning: Vectorized input to `element_text()` is not officially supported.
#> ℹ Results may be unexpected or may change in future versions of ggplot2.
#> → heatmap built with `geom_tile()`

To prevent the reordering, wrap the values with I():

ggheatmap(small_mat) +
    theme(
        axis.text.x = element_text(
            colour = I(c(rep("red", 4), rep("blue", 5)))
        ),
        axis.ticks.x = element_line(
            colour = I(c(rep("red", 4), rep("blue", 5)))
        ),
        axis.ticks.length.x = I(unit(rep(c(1, 4), times = c(4, 5)), "mm"))
    ) +
    anno_top() +
    align_dendro(aes(color = branch), k = 3L) +
    scale_y_continuous(expand = expansion()) &
    theme(plot.margin = margin())
#> Warning: Vectorized input to `element_text()` is not officially supported.
#> ℹ Results may be unexpected or may change in future versions of ggplot2.
#> → heatmap built with `geom_tile()`

When working with facets, manual configuration of the panel using the facet_*() functions is not possible since the internal structure will use facet_grid() to set the row/column groups defined by align_*() functions. However, you can still use facet_grid() or facet_null() (if no panel) to control other arguments except aligned panels (rows in horizontal stack layout or cols in vertical stack layout, or both rows and cols in heatmap body).

A common use case is to modify the panel strip text. The default theme (theme_ggalign()) will always remove the panel strip text, you can override this behaviour with theme(strip.text = element_text()) to add the panel title in the plot area.

ggheatmap(small_mat) +
    facet_grid(labeller = labeller(.column_panel = function(x) letters[as.integer(x)])) +
    theme(strip.text = element_text()) +
    anno_top() +
    align_kmeans(centers = 3L)
#> → heatmap built with `geom_tile()`

Coords

Currently, only cartesian coordinate can be used to align axis well. Internally, the limits will always be set to the number of observations, with an additional range expansion of 0.5 added on both ends.

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 ggplot2_3.5.1
#> 
#> loaded via a namespace (and not attached):
#>  [1] vctrs_0.6.5       cli_3.6.3         knitr_1.49        rlang_1.1.4      
#>  [5] xfun_0.49         generics_0.1.3    textshaping_0.4.0 jsonlite_1.8.9   
#>  [9] labeling_0.4.3    glue_1.8.0        colorspace_2.1-1  htmltools_0.5.8.1
#> [13] ragg_1.3.3        sass_0.4.9        fansi_1.0.6       scales_1.3.0     
#> [17] rmarkdown_2.29    grid_4.4.2        tibble_3.2.1      evaluate_1.0.1   
#> [21] munsell_0.5.1     jquerylib_0.1.4   fastmap_1.2.0     yaml_2.3.10      
#> [25] lifecycle_1.0.4   compiler_4.4.2    dplyr_1.1.4       fs_1.6.5         
#> [29] pkgconfig_2.0.3   farver_2.1.2      systemfonts_1.1.0 digest_0.6.37    
#> [33] R6_2.5.1          tidyselect_1.2.1  utf8_1.2.4        pillar_1.9.0     
#> [37] magrittr_2.0.3    bslib_0.8.0       withr_3.0.2       tools_4.4.2      
#> [41] gtable_0.3.6      pkgdown_2.1.1     cachem_1.1.0      desc_1.4.3