For most annotation functions implemented in ComplexHeatmap, they only draw one same type of annotation graphics, e.g. anno_points()
only draws points. From ComplexHeatmap version 2.9.4, I added a new annotation function anno_customize(), with which you can completely
freely define graphics for every annotation cell.
The input for anno_customize() should be a categorical vector.
library(ComplexHeatmap)
x = c("a", "a", "a", "b", "b", "b", "c", "c", "d", "d")For each level, you need to define a graphics function for it.
graphics = list(
"a" = function(x, y, w, h) grid.rect(x, y, w*0.8, h*0.33, gp = gpar(fill = "red")),
"b" = function(x, y, w, h) grid.text("A", x, y, gp = gpar(col = "darkgreen")),
"c" = function(x, y, w, h) grid.points(x, y, gp = gpar(col = "orange"), pch = 16),
"d" = function(x, y, w, h) {
img = png::readPNG(system.file("extdata", "Rlogo.png", package = "circlize"))
grid.raster(img, x, y, width = unit(0.8, "snpc"), height = unit(0.8, "snpc")*nrow(img)/ncol(img))
}
)When adding graphics, each annotation cell is an independent viewport, thus, the self-defined graphics function accepts four arguments: x and y: the center
of the viewport of the annotation cell, w and h: the width and height of the viewport. In the example above, we set a horizontal bar for "a", a text for "b",
a point for "c" and an image for "d".
Then we add this new annotation to both row and column of the heatmap, just in the same way as normal annotations.
m = matrix(rnorm(100), 10)
Heatmap(m,
top_annotation = HeatmapAnnotation(foo = anno_customize(x, graphics = graphics)),
right_annotation = rowAnnotation(bar = anno_customize(x, graphics = graphics)))
Reordering and splitting are automatically adjusted.
Heatmap(m,
top_annotation = HeatmapAnnotation(foo = anno_customize(x, graphics = graphics)),
right_annotation = rowAnnotation(bar = anno_customize(x, graphics = graphics)),
column_split = x, row_split = x)
Legend() function also accepts a graphics argument, so it is easy to add legends for the “customized annotations”.
m = matrix(rnorm(100), 10)
ht = Heatmap(m,
top_annotation = HeatmapAnnotation(foo = anno_customize(x, graphics = graphics)))
lgd = Legend(title = "foo", at = names(graphics), graphics = graphics)
draw(ht, annotation_legend_list = lgd)
Session info
sessionInfo()## R version 4.1.0 (2021-05-18)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
##
## locale:
## [1] C/UTF-8/C/C/C/C
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] ComplexHeatmap_2.9.4 knitr_1.33
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 highr_0.9 bslib_0.3.0
## [4] compiler_4.1.0 RColorBrewer_1.1-2 jquerylib_0.1.4
## [7] iterators_1.0.13 tools_4.1.0 digest_0.6.27
## [10] clue_0.3-59 jsonlite_1.7.2 evaluate_0.14
## [13] png_0.1-7 rlang_0.4.11 foreach_1.5.1
## [16] magick_2.7.2 yaml_2.2.1 parallel_4.1.0
## [19] blogdown_0.20 xfun_0.24 fastmap_1.1.0
## [22] cluster_2.1.2 stringr_1.4.0 sass_0.4.0
## [25] GlobalOptions_0.1.2 S4Vectors_0.30.0 IRanges_2.26.0
## [28] stats4_4.1.0 R6_2.5.0 GetoptLong_1.0.3
## [31] rmarkdown_2.9 bookdown_0.22 magrittr_2.0.1
## [34] codetools_0.2-18 htmltools_0.5.2 matrixStats_0.59.0
## [37] BiocGenerics_0.38.0 shape_1.4.6 colorspace_2.0-2
## [40] circlize_0.4.14 stringi_1.6.2 doParallel_1.0.16
## [43] crayon_1.4.1 rjson_0.2.20