Cannot figure out how to place legend and annotation differently

[chrmirian]

Hi Zuguang Gu

Thank you for ComplexHeatmap, it is very useful. I am relatively new to programming, so my apologies for this basic question.

I am having problems figuring out how to place legend and annotations differently.

Lets say I have these data

set.seed(123)
library(ComplexHeatmap)
mat = matrix(rnorm(96, 2), 8, 12)
mat = rbind(mat, matrix(rnorm(48, -2), 4, 12))
hmap <- as.data.frame(t(mat))

hmap$type <- rep(c("Ctrl", "Cell_type1", "Cell_type2"), 4)
hmap$malig <- ifelse(hmap$type == "Ctrl", "Ctrl", "Tumor")

hmap_bt <- scale(as.matrix(hmap[, -c(13:14)]))

And used this script

draw(Heatmap(hmap_bt, 
             name = "Z-score",    
             col = colorRamp2(c(-2, 0, 2), c("#6DBCC3", "white", "#8B3A62")),

             show_column_names = FALSE,
             show_column_dend = FALSE,
             column_km = 3,
             
             left_annotation = rowAnnotation(Case = hmap[, c(13:14)]$malig,
                                             Type = hmap[, c(13:14)]$type,
                                             col = list(Case = c("Ctrl" = "#D1B551", "Tumor" = "#678F53"),
                                                        Type = c("Ctrl" = "#D1B551", "Cell_type1" = "green", "Cell_type2" = "blue")),
                                             annotation_legend_param = list(
                                               Case = list( 
                                                 title_gp = gpar(fontsize = 16, 
                                                                 fontface = "bold"), 
                                                 labels_gp = gpar(fontsize = 16)),
                                               Type = list( 
                                                 title_gp = gpar(fontsize = 16,
                                                                 fontface = "bold"), 
                                                 labels_gp = gpar(fontsize = 16)))),
             heatmap_legend_param = list(
               legend_direction = "horizontal", 
               legend_width = unit(6, "cm")), 
    ),

  heatmap_legend_side = "bottom"
)

Which gives this:

I am trying to achieve this graphical output:

This question is also asked on StackOverflow.

Hope that you can help.

Thank you in advance.

Best
Christian

[jokergoo]

I have to say it is a little bit confusing for the design of the package. Because a heatmap can have column annotations as well as row annotations. Row annotations legends are grouped with heatmap legends, which means, heatmap_legend_side controls both row annotation legends and heatmap legend, while annotation_legend_side only controls column annotations. The reason for this design is row annotations can also be independent to heatmaps, such as ht + ha + ha, and in this case, row annotations have the same status as heatmaps, thus the legends are grouped.

If you want to always group annotation legends and heatmap legends separately, you can set legend_grouping = "original" in draw():

draw(Heatmap(hmap_bt, 
             name = "Z-score",    
             col = colorRamp2(c(-2, 0, 2), c("#6DBCC3", "white", "#8B3A62")),

             show_column_names = FALSE,
             show_column_dend = FALSE,
             column_km = 3,
             
             left_annotation = rowAnnotation(Case = hmap[, c(13:14)]$malig,
                                             Type = hmap[, c(13:14)]$type,
                                             col = list(Case = c("Ctrl" = "#D1B551", "Tumor" = "#678F53"),
                                                        Type = c("Ctrl" = "#D1B551", "Cell_type1" = "green", "Cell_type2" = "blue")),
                                             annotation_legend_param = list(
                                               Case = list( 
                                                 title_gp = gpar(fontsize = 16, 
                                                                 fontface = "bold"), 
                                                 labels_gp = gpar(fontsize = 16)),
                                               Type = list( 
                                                 title_gp = gpar(fontsize = 16,
                                                                 fontface = "bold"), 
                                                 labels_gp = gpar(fontsize = 16)))),
             heatmap_legend_param = list(
               legend_direction = "horizontal", 
               legend_width = unit(6, "cm")), 
    ) ,

  heatmap_legend_side = "bottom",
  legend_grouping = "original"
)

Another thing is there is a space between the bottom legend and the heatmap. They should be closer. I will improve it in the future.

[chrmirian]

Thank you, solved it.