Let’s prepare some example data.
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)))
ggheatmap(small_mat) +
scale_fill_viridis_c() +
hmanno("t") +
align_dendro(aes(color = branch), k = 3) +
geom_point(aes(color = branch, y = y)) +
scale_color_brewer(palette = "Dark2") +
ggalign(aes(y = value)) +
geom_boxplot(aes(factor(.x), fill = .panel)) +
scale_fill_brewer(palette = "Dark2")
#> → heatmap built with `geom_tile()`
ggheatmap(small_mat) +
scale_fill_viridis_c() +
hmanno("t", size = 0.5) +
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", size = 0.5) +
align_dendro(aes(color = branch), size = 0.5, k = 4L) +
ggalign(aes(x = value), data = rowSums) +
geom_bar(
aes(y = .y, fill = factor(.y)),
stat = "identity",
orientation = "y"
) +
scale_fill_brewer(name = NULL, palette = "Paired", guide = "none")
#> → heatmap built with `geom_tile()`
(ggstack(small_mat) +
ggheatmap() +
ggheatmap() &
scale_fill_viridis_c() &
theme(axis.text.x = element_text(angle = -60, hjust = 0))) +
stack_active() +
align_dendro(aes(color = branch), k = 4L, size = 0.2) +
scale_color_brewer(palette = "Dark2")
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`
ggstack(small_mat, "v") +
align_dendro(aes(color = branch),
k = 4L, size = 0.2,
theme = theme(axis.text.x = element_blank())
) +
scale_color_brewer(palette = "Dark2") +
ggheatmap() +
ggheatmap() &
scale_fill_viridis_c() &
theme(axis.text.x = element_text(angle = -60, hjust = 0))
#> Warning: The `theme` argument of `align_dendro()` is deprecated as of ggalign 0.0.5.
#> ℹ Please use the `action` argument instead.
#> ℹ The deprecated feature was likely used in the ggalign package.
#> Please report the issue at <https://github.com/Yunuuuu/ggalign/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`
sessionInfo()
#> R version 4.4.1 (2024-06-14)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 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-r0.3.26.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] ggalign_0.0.4.9000 ggplot2_3.5.1 rmarkdown_2.28
#>
#> loaded via a namespace (and not attached):
#> [1] crayon_1.5.3 vctrs_0.6.5 cli_3.6.3 knitr_1.48
#> [5] rlang_1.1.4 xfun_0.48 highr_0.11 jsonlite_1.8.9
#> [9] labeling_0.4.3 glue_1.8.0 colorspace_2.1-1 buildtools_1.0.0
#> [13] htmltools_0.5.8.1 maketools_1.3.1 sys_3.4.3 sass_0.4.9
#> [17] fansi_1.0.6 scales_1.3.0 grid_4.4.1 tibble_3.2.1
#> [21] evaluate_1.0.1 munsell_0.5.1 jquerylib_0.1.4 fastmap_1.2.0
#> [25] yaml_2.3.10 lifecycle_1.0.4 compiler_4.4.1 RColorBrewer_1.1-3
#> [29] pkgconfig_2.0.3 farver_2.1.2 digest_0.6.37 viridisLite_0.4.2
#> [33] R6_2.5.1 utf8_1.2.4 pillar_1.9.0 magrittr_2.0.3
#> [37] bslib_0.8.0 withr_3.0.1 tools_4.4.1 gtable_0.3.5
#> [41] cachem_1.1.0