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Quad-Layout

Source: vignettes/articles/quad-layout.Rmd
quad-layout.Rmd

As discussed in vignette("heatmap-layout"), the ggheatmap() function is a specialized form of quad_layout(). Specifically, it is a variant of quad_alignb(), which aligns observations both horizontally and vertically.

quad_layout() arranges plots in the Quad-Side of a main plot. Depending on whether you want to align observations in the horizontal or vertical direction, there are four main types of quad_layout(): - quad_free/ggside: Never align observations. - quad_alignh: Align observations in the horizontal direction. - quad_alignv: Align observations in the vertical direction. - quad_alignb: Align observations in both horizontal and vertical directions.

library(ggalign)
#> Loading required package: ggplot2

quad_free()

quad_free() won’t align observations. ggside() is an alias of quad_free(). It do the same function of ggside packge. This is particularly useful for metadata for summary graphics on a continuous axis

input data

Like ggplot, you’ll need to provide input that can be converted into a data frame. Internally, the fortify_data_frame() function is used to handle this conversion.

ggside(mpg) +
    geom_point(aes(displ, hwy, colour = class))

annotation

Like ggheatmap(), annotations in quad_free() can be placed at the top, left, bottom, and right sides, but all annotations here use stack_free(), meaning they don’t align observations. The data will be directly inherited which is different from the quad_alignb()/quad_alignh()/quad_alignv() where the column annotation will transpose the layout matrix

Additionally, annotations can be manually initialized with user-specified data using quad_init(), I’ll demonstrate it in quad_alignh()/quad_alignv() section where manual initialization is required.

ggside(mpg, aes(displ, hwy, colour = class)) -
    # set default theme for all plots in the layout
    plot_theme(theme_bw()) +
    geom_point(size = 2) +
    # add top annotation
    anno_top(size = 0.3) -
    # set default theme for the top annotation
    plot_theme(theme_no_axes("tb")) +
    # add a plot in the top annotation
    ggfree() +
    geom_density(aes(displ, y = after_stat(density), colour = class), position = "stack") +
    # add right annotation
    anno_right(size = 0.3) -
    # set default theme for the right annotation
    plot_theme(theme_no_axes("lr")) +
    # add a plot in the right annotation
    ggfree() +
    geom_density(aes(x = after_stat(density), hwy, colour = class),
        position = "stack"
    ) +
    theme(axis.text.x = element_text(angle = 90, vjust = .5))

Unlike ggheatmap()/heatmap_layout(), ggside()/quad_free() allows facetting for the main plot, which should also be applied to the annotations for proper alignment.

i2 <- iris
i2$Species2 <- rep(c("A", "B"), 75)
ggside(i2, aes(Sepal.Width, Sepal.Length, color = Species)) -
    # set default theme for all plots in the layout
    plot_theme(theme_bw()) +
    geom_point(size = 2) +
    facet_grid(Species ~ Species2) +
    # add top annotation
    anno_top(size = 0.3) -
    # set default theme for the top annotation
    plot_theme(theme_no_axes("tb")) +
    # add a plot in the top annotation
    ggfree() +
    geom_density(aes(Sepal.Width, y = after_stat(density), colour = Species),
        position = "stack"
    ) -
    # we can utilize the `-` to set facet for all plots in the annotation
    facet_grid(cols = vars(Species2)) +
    # add right annotation
    anno_right(size = 0.3) -
    # set default theme for the right annotation
    plot_theme(theme_no_axes("lr")) +
    # add a plot in the right annotation
    ggfree() +
    geom_density(aes(x = after_stat(density), Sepal.Length, colour = Species),
        position = "stack"
    ) +
    theme(axis.text.x = element_text(angle = 90, vjust = .5)) -
    # we can utilize the `-` to set facet for all plots in the annotation
    facet_grid(rows = vars(Species))

quad_alignh()/quad_alignv()

quad_alignh() aligns observations horizontally, while quad_alignv() aligns observations vertically.

input data

To align observations in the horizontal/vertical direction, you’ll need to provide input that can be converted into a matrix. Internally, the fortify_matrix() function is used to handle this conversion, ensuring the input is in the correct format for alignment.

The underlying ggplot data is the same with ggheatmap()/heatmap_layout(), it is recommended to use .y, or .row_names as the y mapping in the main plot for quad_alignh() but use .x or .column_names as the x mapping in the main plot for quad_alignv().

set.seed(123)
small_mat <- matrix(rnorm(56), nrow = 8)
rownames(small_mat) <- paste0("row", seq_len(nrow(small_mat)))
colnames(small_mat) <- paste0("column", seq_len(ncol(small_mat)))
# we'll align the horizontal direction
quad_alignh(small_mat) +
    geom_boxplot(aes(value, .row_names, fill = .row_names)) +
    scale_fill_brewer(palette = "Dark2")

# we'll align the vertical direction
quad_alignv(small_mat) +
    geom_boxplot(aes(.column_names, value, fill = .column_names)) +
    scale_fill_brewer(palette = "Dark2")

annotation

the same with ggheatmap()/heatmap_layout(), we can add annotation in top, left, bottom, and right side. but the top and bottom annotation in quad_alignh() is a stack_free() which won’t align observations and left and right annotation in quad_alignv() is a stack_free() which won’t align observations.

For left and right annotation in quad_alignh(), they are a stack_align() layout which will align observations, and require a matrix in the layout data. So it can inherit from the parent quad_layout() and we can add both ggalign() and ggfree() and other align_*() functions to the annotation.

quad_alignh(small_mat) +
    geom_boxplot(aes(value, .row_names, fill = .row_names)) +
    scale_fill_brewer(palette = "Dark2") +
    anno_left() +
    align_dendro()

For top and bottom annotation in quad_alignh(), they are a stack_free() which won’t align observations, and require a data frame in the layout data. In this way, we won’t transform the matrix to a data frame and always prevent user from inheriting from the parent layout matrix.

quad_alignh(small_mat) +
    geom_boxplot(aes(value, .row_names, fill = .row_names)) +
    scale_fill_brewer(palette = "Dark2") +
    anno_top()
#> Error in `quad_layout_add()`:
#> ! Cannot initialize the top annotation stack.
#> ℹ `data` in `quad_alignh()` is a double matrix, but we need a <data.frame>.
#> ℹ Try using `quad_init()` to initialize the top annotation with self-customized
#>   data.

Manual initialization of annotations with quad_init() is required in such cases:

quad_alignh(small_mat) +
    geom_boxplot(aes(value, .row_names, fill = .row_names)) +
    scale_fill_brewer(palette = "Dark2") +
    # initialize the top annotation with a self-defined data frame
    quad_init("top", data = mpg) +
    # add a plot in the top annotation
    ggfree(aes(displ, hwy, colour = class)) +
    geom_point(aes(displ, hwy, colour = class))

The same with quad_alignh(), we need to manually initialize the left and right annotations in quad_alignv().

quad_alignv(small_mat) +
    geom_boxplot(aes(.column_names, value, fill = .column_names)) +
    scale_fill_brewer(palette = "Dark2") +
    # initialize the left annotation with a self-defined data frame
    quad_init("left", data = mpg) +
    # add a plot in the top annotation
    ggfree(aes(displ, hwy, colour = class)) +
    geom_point(aes(displ, hwy, colour = class))

quad_alignb()

quad_alignb aligns observations in both horizontal and vertical directions. It is a base version of ggheatmap()/heatmap_layout(), it won’t add the main plot geoms and default mapping automatically.

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