Home | Blog | Software | Publications | GitHub


Merge heatmap and annotation legends into a same column

In ComplexHeatmap package, legends for heatmap and annotations are differently treated and they will be put in different places. However, if there are not too many heatmaps and annotations, separating these two types of legends will be kind of waste of spaces.

In draw() method of HeatmapList class, there is an option heatmap_legend_list (or annotation_legend_list) which accepts additional self-defined legends (in a form of grob objects). Thus, one strategy to merge heatmap legends and annotation legends is to extract the legends first and suppress plotting legends, later we construct a list of legends and send to heatmap_legend_list argument.

In following example, there is only one heatmap and two simple column annotations. When constructing column annotaiton ha, show_legend is set to FALSE to suppress annotation legends.

library(ComplexHeatmap)
library(circlize)
df = data.frame(type = c(rep("a", 5), rep("b", 5)),
                age = sample(1:20, 10))

ha = HeatmapAnnotation(df = df,
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))),
    show_legend = FALSE
)

Color mapping information is stored in ha and we can extract legends from ha object.

anno_legend_list = lapply(ha@anno_list[c("type", "age")], 
    function(anno) color_mapping_legend(anno@color_mapping, plot = FALSE))
anno_legend_list
## $type
## frame[GRID.frame.559] 
## 
## $age
## frame[GRID.frame.574]

Similar, show_heatmap_legend is set to FALSE when creating ht and legend object is extracted afterwards.

mat = matrix(rnorm(80, 2), 8, 10)
ht = Heatmap(mat, name = "ht", top_annotation = ha, show_heatmap_legend = FALSE)
heatmap_legend = color_mapping_legend(ht@matrix_color_mapping, plot = FALSE)

Finally, draw() is called explicitely and a list of both heatmap legend and annotation legends are sent to heatmap_legend_list argument.

draw(ht, heatmap_legend_list = c(anno_legend_list, list(heatmap_legend)))

plot of chunk unnamed-chunk-5