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I have created a ComplexHeatmap containing 2 Heatmaps, each with their own legend. The legend on the first Heatmap is continuous, whereas that of the second is discrete.

When I concatenate these Heatmaps vertically, and draw the HeatmapList, their legends are auto-aligned to the center of the plot. Is there any way I can have these legends positioned centered to the respective heatmaps and not to the center of the plot?

This is what I have:

Current_Image

Here's what I'd like to have:

Desired_Image

How can I go about solving this problem? I'd really like to avoid creating customized Legends if I can, but if that's what it takes, that works too.

Thank you in advance for any help/pointers!

Note: I tried adding the ComplexHeatmap tag, but it doesn't exist yet and I don't have the reputation to create new tags yet.

Edit: Since this is a Bioconductor package, I also created an identical post on the Bioconductor support forum

Dummy data and code:

devtools::install_github('jokergoo/ComplexHeatmap');
library(ComplexHeatmap);
library(viridis);

dummy_top_mat <- structure(c(0.4563, 0.2211, 1.2235, 0.067, 1.6859, 1.0936, 0.4533, 
1.6844, 1.0039, 0.5402, 0.6841, 1.498, 1.042, 0.1711, 0.3565, 
2.2814, 3.0516, 1.5012, 0.5367, 3.0846, 1.1909, 0.235, 1.4266, 
0.4858, 2.9054, 0.3733, 0.6902, 0.8555, 0.4234, 2.6778, 0.1568, 
0.5556, 2.0172, 0.8034, 2.2897, 0.1166, 3.8033, 0.1431, 2.0606, 
1.2725, 1.5365, 0.4123, 1.2087, 1.1264, 0.8334, 1.1943, 1.58, 
1.5849, 0.3004, 0.3722, 0.0362, 0.0532, 1.4867, 0.4053, 0.3615, 
0.0897, 1.3217, 1.1447, 1.3058, 0.1903, 0.1067, 0.9482, 1.3382, 
3.2955, 0.391, 1.0418, 0.2041, 1.208, 1.5857, 3.5313, 0.472, 
1.389, 0.2143, 0.0226, 0.029, 0.444, 2.0521, 0.3955, 0.3495, 
0.5062, 1.3236, 1.3234, 0.7111, 0.1176, 2.2223, 1.2073, 0.3964, 
2.1175, 0.3382, 0.2816, 0.71, 3.1417, 0.2402, 0.5793, 0.7662, 
1.6782, 0.0986, 0.087, 0.5447, 2.6672, 1.2498, 1.0676, 1.8608, 
1.8146, 0.1422, 0.4221, 0.0303, 0.9541, 0.7358, 1.7664, 1.5144, 
0.2034, 0.9366, 0.7837, 0.3284, 0.1477, 1.8306, 1.3564, 0.1126, 
0.0171, 2.9858, 0.0233, 0.2796, 0.6995, 1.6081, 0.215, 1.7093, 
0.5178, 1.7061, 2.473, 1.8912, 0.7661, 4.4102, 1.2963, 0.6542, 
0.4281, 0.4491, 0.6, 0.4076, 1.6869, 0.4747, 3.9823, 1.1226, 
2.7355, 2.7036, 0.2241, 0.983, 1.0992, 1.4736, 0.1584, 0.2995, 
0.2272, 0.5744, 0.9314, 0.6924, 0.0812, 1.361, 0.727, 0.1525, 
1.3367, 0.566, 2.7801, 0.2349, 3.2655, 1.0675, 0.449, 0.5411, 
0.8291, 0.52, 0.0507, 0.6538, 0.4636, 1.2063, 0.9784, 0.1925, 
0.0756, 0.136, 1.2529, 0.317, 0.0281, 0.8668, 3.4138, 5.3898, 
0.521, 0.087, 3.4819, 0.1114, 0.0061, 0.9804, 1.139, 1.4159, 
1.0297, 0.6503, 1.0828, 2.3527, 0.057, 0.5602, 0.4017, 0.9985, 
0.8673), .Dim = c(10L, 20L), .Dimnames = list(c("gene01", "gene02", 
"gene03", "gene04", "gene05", "gene06", "gene07", "gene08", "gene09", 
"gene10"), c("sample01", "sample02", "sample03", "sample04", 
"sample05", "sample06", "sample07", "sample08", "sample09", "sample10", 
"sample11", "sample12", "sample13", "sample14", "sample15", "sample16", 
"sample17", "sample18", "sample19", "sample20")));

dummy_bottom_mat <- structure(c("Positive", "Positive", "Positive", "Positive", "Negative", 
"Positive", "Positive", "Positive", "Positive", "Negative", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Negative", "Positive", 
"Negative", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Negative", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Negative", "Positive", "Positive", "Positive", "Negative", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Negative", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Negative", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive", "Positive", "Positive", "Positive", "Positive", "Positive", 
"Positive"), .Dim = c(6L, 20L), .Dimnames = list(c("marker1", 
"marker2", "marker3", "marker4", "marker5", "marker6"), c("sample01", 
"sample02", "sample03", "sample04", "sample05", "sample06", "sample07", 
"sample08", "sample09", "sample10", "sample11", "sample12", "sample13", 
"sample14", "sample15", "sample16", "sample17", "sample18", "sample19", 
"sample20")));

hmap1 <- Heatmap(dummy_top_mat, col = colorRampPalette(viridis(15))(100), name = 'log2 (TPM)', na_col = 'grey60', cluster_rows = FALSE, cluster_columns = FALSE, row_names_side = 'left', column_title_side = 'top', rect_gp = gpar(col='white', lwd=0.5), height=unit(10*0.75,'cm'), width = unit(20*0.75, 'cm'), column_title = 'Gene Expression');

hmap2 <- Heatmap(dummy_bottom_mat, col = c('Negative'='red', 'Positive'='blue'), na_col = 'grey60', row_split = factor( c('gp1','gp1','gp1','gp1','gp2','gp2'), c('gp1','gp2'), ordered = TRUE), name = 'Marker\nStatus', rect_gp = gpar(col='white',lwd=1), row_title = NULL, height = unit(6*0.75,'cm'), width = unit(20*0.75, 'cm'), row_names_side = 'left', column_title = 'Biomarkers');

draw(hmap1 %v% hmap2, ht_gap = unit(1, 'cm'), auto_adjust = FALSE);

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS  10.14.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Users/ram/miniconda3/lib/R/lib/libRblas.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] viridis_0.5.1        viridisLite_0.3.0    ComplexHeatmap_2.1.0 forcats_0.4.0       
 [5] stringr_1.4.0        dplyr_0.8.0.1        purrr_0.2.5          readr_1.3.1         
 [9] tidyr_0.8.3          tibble_2.1.1         ggplot2_3.1.1        tidyverse_1.2.1     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0          lubridate_1.7.4     lattice_0.20-38     circlize_0.4.6      prettyunits_1.0.2  
 [6] png_0.1-7           ps_1.3.0            rprojroot_1.3-2     assertthat_0.2.1    digest_0.6.18      
[11] R6_2.3.0            cellranger_1.1.0    plyr_1.8.4          backports_1.1.4     reprex_0.2.1       
[16] httr_1.4.0          pillar_1.3.1        GlobalOptions_0.1.0 rlang_0.3.1         lazyeval_0.2.2     
[21] readxl_1.3.1        rstudioapi_0.10     callr_3.2.0         GetoptLong_0.1.7    desc_1.2.0         
[26] devtools_2.0.2      munsell_0.5.0       broom_0.5.2         compiler_3.5.1      modelr_0.1.4       
[31] pkgconfig_2.0.2     pkgbuild_1.0.3      shape_1.4.4         tidyselect_0.2.5    gridExtra_2.3      
[36] crayon_1.3.4        withr_2.1.2         nlme_3.1-137        jsonlite_1.6        gtable_0.3.0       
[41] magrittr_1.5        scales_1.0.0        cli_1.1.0           stringi_1.4.3       remotes_2.0.4      
[46] fs_1.3.1            xml2_1.2.0          generics_0.0.2      rjson_0.2.20        RColorBrewer_1.1-2 
[51] tools_3.5.1         glue_1.3.0          hms_0.4.2           processx_3.3.1      pkgload_1.0.2      
[56] parallel_3.5.1      clue_0.3-57         colorspace_1.4-1    cluster_2.0.7-1     sessioninfo_1.1.1  
[61] rvest_0.3.3         memoise_1.1.0       haven_2.1.0         usethis_1.5.0
Improve this question
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    $\begingroup$ I think this is more suitable for GitHub issues "feature request". Currently if we add legends manually using draw(..., Legend(), ...) then we can use "just" argument within draw() to define position. But if we want to adjust existing legend within Heatmap function using Heatmap(..., heatmap_legend_param = list( it doesn't have "just" argument. (See 5.4 Section of the manual). $\endgroup$
    – zx8754
    Commented May 13, 2019 at 6:10
  • $\begingroup$ Even with just, it seems to be more along the lines of "where in the image" than "where with respect to the heatmap this legend belongs to". I will open a GitHub issue though, maybe the dev has a line of thought for this. $\endgroup$
    – Ram RS
    Commented May 13, 2019 at 10:35
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    $\begingroup$ Here's the issue I opened on GitHub: github.com/jokergoo/ComplexHeatmap/issues/317 $\endgroup$
    – Ram RS
    Commented May 13, 2019 at 13:40

1 Answer 1

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Turns out, this is not possible. Concatenating two heatmaps causes their legends to be grouped, and while they can be positioned together at the top, bottom, at the left or the right sides, they cannot be separated spatially.

The discussion can be viewed at the bioconductor support link from the question. Relevant snippets:

No, since you put the two heatmaps as one plot, the legends are grouped. You can either edit in Inkscape or make two heatmaps in two plots. You can get the column (order) of the first heatmap ... and assign to the second heatmap

 

The thing is if you add two heatmaps, the legends are always plotted together. One way I can think to improve this is to move the legends to the bottom of the heatmap.

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    $\begingroup$ Thanks for replying $\endgroup$
    – M__ ♦
    Commented May 15, 2019 at 19:33

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