Let’s prepare some example data.
set.seed(123)
small_mat <- matrix(rnorm(72), nrow = 9)
rownames(small_mat) <- paste0("row", seq_len(nrow(small_mat)))
colnames(small_mat) <- paste0("column", seq_len(ncol(small_mat)))
heatmap layout customize
Based on dendrogram
ggheatmap(small_mat) +
anno_top() +
align_dendro(aes(color = branch), k = 3) +
geom_point(aes(color = branch, y = y)) +
scale_color_brewer(palette = "Dark2")
#> → heatmap built with `geom_tile()`
Based on kmeans
ggheatmap(small_mat) +
anno_top() +
align_kmeans(3L)
#> → heatmap built with `geom_tile()`
Based on a group variable
ggheatmap(small_mat) +
anno_top() +
align_group(sample(letters[1:4], ncol(small_mat), replace = TRUE))
#> → heatmap built with `geom_tile()`
Based on an ordering weights
Here, we ordered the heatmap rows based on the row means.
ggheatmap(small_mat) +
anno_left() +
align_order(rowMeans)
#> → heatmap built with `geom_tile()`
Heatmap annotation plot
ggheatmap(small_mat) +
anno_top() +
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) +
anno_top(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") +
anno_left(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()`
Multiple heatmaps
Horizontal layout
(stack_alignh(small_mat) +
ggheatmap() +
ggheatmap() &
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()`
Vertical layout
stack_alignv(small_mat) -
plot_theme(
axis.text.x = element_blank(),
axis.ticks.x = element_blank()
) +
align_dendro(aes(color = branch), k = 4L, size = 0.2) +
scale_color_brewer(palette = "Dark2") +
ggheatmap() +
ggheatmap() +
theme(axis.text.x = element_text(angle = -60, hjust = 0))
#> → heatmap built with `geom_tile()`
#> → heatmap built with `geom_tile()`
marginal plots
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") +
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)) &
scale_color_brewer(palette = "Dark2")
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