Heatmap and Annotation Legends

Author: Zuguang Gu ( z.gu@dkfz.de )

Date: 2016-10-17

The legends for heatmaps are composed with a color bar, labels and titles. ComplexHeatmap automatically generates legends according to the input matrix and annotations, while also provide flexibility to customize and add new legends.

Basic settings

Legends for all heatmaps and row annotations are drawn together and legends for all column annotations are drawn together. The legends for heatmaps and legends for annotations are put in independent viewports.

library(ComplexHeatmap)
library(circlize)

set.seed(123)
mat = matrix(rnorm(80, 2), 8, 10)
mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
rownames(mat) = paste0("R", 1:12)
colnames(mat) = paste0("C", 1:10)

ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep("a", 5), rep("b", 5))), 
    col = list(type1 = c("a" =  "red", "b" = "blue")))
ha_row = rowAnnotation(df = data.frame(type2 = c(rep("A", 6), rep("B", 6))), 
    col = list(type2 = c("A" =  "green", "B" = "orange")), width = unit(1, "cm"))

ht1 = Heatmap(mat, name = "ht1", column_title = "Heatmap 1", top_annotation = ha_column)
ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2")
ht_list = ht1 + ht2 + ha_row

draw(ht_list)

plot of chunk legend_default

Side of legends can be set by heatmap_legend_side and annotation_legend_side.

draw(ht_list, heatmap_legend_side = "left", annotation_legend_side = "bottom")

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show_heatmap_legend and show_annotation_legend set visibility of legends.

draw(ht_list, show_heatmap_legend = FALSE, show_annotation_legend = FALSE)

plot of chunk legend_show

You can choose to only show some of the heatmap legends by setting show_heatmap_legend to a logical value when constructing single heatmaps. Also HeatmapAnnotation() (or the shortcut function columnAnnotation() and rowAnnotation()) provides show_legend argument to control visibility of annotation legends.

ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep("a", 5), rep("b", 5))), 
    col = list(type1 = c("a" =  "red", "b" = "blue")), show_legend = FALSE)
ha_row = rowAnnotation(df = data.frame(type2 = c(rep("A", 6), rep("B", 6))), 
    col = list(type2 = c("A" =  "green", "B" = "orange")), show_legend = FALSE, width = unit(1, "cm"))

ht1 = Heatmap(mat, name = "ht1", column_title = "Heatmap 1", top_annotation = ha_column)
ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2", show_heatmap_legend = FALSE)
ht1 + ht2 + ha_row

plot of chunk legend_show_part

Customization of legends

Legend itself can be flexibly customized. Parameters for making the legend can be set by heatmap_legend_param (for heatmap) or annotation_legend_param (for annotations). The parameters that can be set are as follows:

title: title of the legend
title_gp: graphic parameters for the legend title
title_position: position of title relative to the legend, possible values are topcenter, topleft, leftcenter, lefttop.
color_bar: style of the color bar, i.e. continuous or discrete
grid_height: height of the small grid in the color bar, only works for discrete color bar
grid_width: width of the color bar
grid_border: border of the color bar
at: break values shown on the legend
labels: labels which correspond to the breaks values
labels_gp: graphic parameters for legend labels
nrow and ncol: if there are too many legends, they can be put into an array. These two parameters controls number of rows or columns
legend_direction: when color_bar is set to continuous, it controls the direction of the legend, possible values are vertical and horizontal
legend_width and legend_height: when color_bar is continuous, the width or height of the legend

Following example changes the default graphic parameters for labels and titles:

df = data.frame(type = c(rep("a", 5), rep("b", 5)))
ha = HeatmapAnnotation(df = df, col = list(type = c("a" =  "red", "b" = "blue")),
    annotation_legend_param = list(type = list(title = "TYPE", title_gp = gpar(fontsize = 14), 
                                               labels_gp = gpar(fontsize = 8))))
ht1 = Heatmap(mat, name = "ht1", column_title = "Heatmap 1", top_annotation = ha)
ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2", 
    heatmap_legend_param = list(title = "Heatmap2", title_gp = gpar(fontsize = 8), 
        labels_gp = gpar(fontsize = 14)))
ht1 + ht2

plot of chunk heatmap_list_advanced

You can specify break values and break labels (both for character values and numeric values) by at and labels in corresponding heatmap_legend_param and annotation_legend_param. Note at can also be character break values.

ha = HeatmapAnnotation(df = df, col = list(type = c("a" =  "red", "b" = "blue")),
    annotation_legend_param = list(type = list(title = "TYPE", title_gp = gpar(fontsize = 14), 
        labels_gp = gpar(fontsize = 8), at = c("a", "b"), labels = c("A", "B"))))
ht1 = Heatmap(mat, name = "ht1", column_title = "Heatmap 1", top_annotation = ha,
    heatmap_legend_param = list(at = c(-3, 0, 3), labels = c("-three", "zero", "+three")))
ht1 + ht2

plot of chunk self_define_heatmap_legend

If you have many levels in your annotation or matrix, you can put all levels into an array by specifying nrow or ncol:

ha_chr = rowAnnotation(chr = sample(paste0("chr", 1:20), nrow(mat), replace = TRUE),
    annotation_legend_param = list(chr = list(ncol = 2, title = "chromosome", title_position = "topcenter")),
    width = unit(5, "mm"))
ht1 = Heatmap(mat, name = "ht1")
ht1 + ha_chr

plot of chunk unnamed-chunk-1

Or put at bottom of the heatmap:

ha_chr = rowAnnotation(chr = sample(paste0("chr", 1:20), nrow(mat), replace = TRUE),
    annotation_legend_param = list(chr = list(nrow = 2, title = "chr", title_position = "leftcenter")),
    width = unit(5, "mm"))
ht1 = Heatmap(mat, name = "ht1", show_heatmap_legend = FALSE)
draw(ht1 + ha_chr, heatmap_legend_side = "bottom")

plot of chunk unnamed-chunk-2

If you don't like the default discrete color bar for continuous values, you can specify color_bar to continuous. For the simple annotation which contains continuous values, color_bar can also be set to continuous.

ha = HeatmapAnnotation(df = data.frame(value = runif(10)), 
    col = list(value = colorRamp2(c(0, 1), c("white", "blue"))), 
    annotation_legend_param = list(color_bar = "continuous", at = c(0, 0.5, 1), 
        labels = c("low", "median", "high"), legend_height = unit(4, "cm")))
Heatmap(mat, name = "ht1", top_annotation = ha, heatmap_legend_param = list(color_bar = "continuous"))

plot of chunk unnamed-chunk-3

Some users prefer to put the legend at the bottom of heatmaps.

ht = Heatmap(mat, name = "ht1", heatmap_legend_param = list(color_bar = "continuous", legend_direction = "horizontal",
    legend_width = unit(5, "cm"), title_position = "lefttop"))
draw(ht, heatmap_legend_side = "bottom")

plot of chunk unnamed-chunk-4

If you want to change default settings for all heatmaps/annotations, you can set it globally by ht_global_opt().

ht_global_opt(heatmap_legend_title_gp = gpar(fontsize = 16), annotation_legend_labels_gp = gpar(fontface = "italic"))
ha = HeatmapAnnotation(df = data.frame(value = runif(10)), 
    col = list(value = colorRamp2(c(0, 1), c("white", "blue"))), 
    annotation_legend_param = list(color_bar = "continuous"))
ht1 = Heatmap(mat, name = "ht1", column_title = "Heatmap 1", top_annotation = ha)
ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2", heatmap_legend_param = list(title_gp = gpar(fontsize = 8)))
ht1 + ht2

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ht_global_opt(RESET = TRUE)

Add new legends

ComplexHeatmap only generates legends for heatmaps and simple annotations. Self-defined legends can be passed by heatmap_legend_list and annotation_legend_list as a list of grob objects.

grid package provides legendGrob() to construct a legend grob with certain style but styles are still limited. For advanced users, they can construct a legend grob totally from ground by frameGrob() and placeGrob().

ha = HeatmapAnnotation(points = anno_points(rnorm(10)))
ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2", top_annotation = ha, show_heatmap_legend = FALSE)
lgd = legendGrob(c("dots"), pch = 16)
draw(ht1 + ht2, annotation_legend_list = list(lgd))

plot of chunk self_defined_annotation_legend

From version 1.9.7, ComplexHeatmap package provides a Legend() function which can produce legends in grob formats (actually all legends in the package are implemented by Legend() function). In following example, we have several column annotations which contains points and we also want to show legends for these non-heatmap graphics.

ha = HeatmapAnnotation(points = anno_points(rnorm(10), gp = gpar(col = rep(2:3, each = 5))))
ht = Heatmap(mat, name = "ht2", column_title = "Heatmap 2", top_annotation = ha)
lgd = Legend(at = c("class1", "class2"), title = "points", type = "points", legend_gp = gpar(col = 2:3))
draw(ht, annotation_legend_list = list(lgd))

plot of chunk unnamed-chunk-6

Also check this blog link for more demonstrations.

Session info

sessionInfo()

## R version 3.3.1 (2016-06-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.1 LTS
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
##  [4] LC_COLLATE=C               LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
## [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] stats4    parallel  grid      stats     graphics  grDevices utils     datasets  methods  
## [10] base     
## 
## other attached packages:
##  [1] dendextend_1.3.0      dendsort_0.3.3        cluster_2.0.5         HilbertCurve_1.4.0   
##  [5] GenomicRanges_1.26.0  GenomeInfoDb_1.10.0   IRanges_2.8.0         S4Vectors_0.12.0     
##  [9] BiocGenerics_0.20.0   circlize_0.3.9        ComplexHeatmap_1.12.0 knitr_1.14           
## [13] markdown_0.7.7       
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.7          XVector_0.14.0       DEoptimR_1.0-6       formatR_1.4         
##  [5] RColorBrewer_1.1-2   plyr_1.8.4           HilbertVis_1.32.0    zlibbioc_1.20.0     
##  [9] class_7.3-14         tools_3.3.1          prabclus_2.2-6       mclust_5.2          
## [13] evaluate_0.10        gtable_0.2.0         lattice_0.20-34      png_0.1-7           
## [17] mvtnorm_1.0-5        trimcluster_0.1-2    stringr_1.1.0        GlobalOptions_0.0.10
## [21] fpc_2.1-10           diptest_0.75-7       nnet_7.3-12          robustbase_0.92-6   
## [25] GetoptLong_0.1.5     flexmix_2.3-13       fastcluster_1.1.21   ggplot2_2.1.0       
## [29] kernlab_0.9-25       magrittr_1.5         whisker_0.3-2        scales_0.4.0        
## [33] modeltools_0.2-21    MASS_7.3-45          mime_0.5             shape_1.4.2         
## [37] colorspace_1.2-7     stringi_1.1.2        munsell_0.4.3        rjson_0.2.15