Create colored rectangle annotations for categorical data

Similar to anno_simple but with individual boxes!

anno_cat(
  x,
  which,
  renamer = identity,
  col = distinct_palette(),
  width = NULL,
  height = NULL,
  box_col = "white",
  box_lwd = 0.5,
  border_col = NA,
  border_lwd = 1,
  legend = TRUE,
  legend_title = ""
)

Arguments

x

data vector, treated as categorical

which

Whether it is a column annotation or a row annotation?

renamer

function renaming variable values for legend

col

colors vector, at least as long as unique(x), optionally named by x levels

width

grid unit object or NULL

height

grid unit object or NULL

box_col

colour of boxes around individual cells

box_lwd

line width of boxes around individual cells

border_col

colour of border around all cells

border_lwd

line width of border around all cells

legend

generate legend for this annotation (attached as attribute of heatmap, and not automatically included in plot)

legend_title

title for legend, if drawn

Value

AnnotationFunction

Examples

library(ComplexHeatmap)
#> Loading required package: grid
#> ========================================
#> ComplexHeatmap version 2.18.0
#> Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
#> Github page: https://github.com/jokergoo/ComplexHeatmap
#> Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
#> 
#> If you use it in published research, please cite either one:
#> - Gu, Z. Complex Heatmap Visualization. iMeta 2022.
#> - Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
#>     genomic data. Bioinformatics 2016.
#> 
#> 
#> The new InteractiveComplexHeatmap package can directly export static 
#> complex heatmaps into an interactive Shiny app with zero effort. Have a try!
#> 
#> This message can be suppressed by:
#>   suppressPackageStartupMessages(library(ComplexHeatmap))
#> ========================================
# draw the annotation without a heatmap, you will never normally do this!
vp <- viewport(width = 0.75, height = 0.75)

grid::grid.newpage()
pushViewport(vp)
cats <- letters[1:4]
draw(anno_cat(cats, which = "row"))


grid::grid.newpage()
pushViewport(vp)
draw(
  anno_cat(
    x = cats, col = structure(names = cats, 1:4), which = "column",
    box_col = "black", box_lwd = 5
  )
)


# developer note #
# list of annotations can be split and ordered (adding NULL makes a list)
# https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html
# (section #4.8 concatenate-only-the-annotations)
grid::grid.newpage()
pushViewport(vp)

annoList <- rowAnnotation(
  hi = anno_cat(cats, which = "row", border_col = "black")
) +
  NULL
draw(object = annoList, row_split = c(1, 1:3), row_order = 4:1)
pushViewport(viewport(x = 0.6))
draw(anno_cat(cats, "row", legend_title = "abcd") %>% attr("Legend"))