Last updated: 2023-11-01

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File Version Author Date Message
Rmd 3e13eb5 Dave Tang 2023-11-01 ComplexHeatmap

Install latest version from GitHub.

remotes::install_github("jokergoo/ComplexHeatmap")

Load library.

library(ComplexHeatmap)

Download example data.

example_file <- "https://davetang.org/file/TagSeqExample.tab"
data <- read.delim(example_file, header = TRUE, row.names = "gene")
data_subset <- as.matrix(data[rowSums(data)>50000,])
dim(data_subset)
[1] 49  6

Default heatmap for ComplexHeatmap.

Heatmap(data_subset)

Normalise using z-score.

cal_z_score <- function(x){
  (x - mean(x)) / sd(x)
}

data_subset_norm <- t(apply(data_subset, 1, cal_z_score))
Heatmap(data_subset_norm)

Add a title using column_title; the name parameter puts a title of the heatmap legend.

Heatmap(data_subset_norm, column_title = "My title", name = "Legend")

Two heatmaps.

one <- Heatmap(data_subset, column_title = "Raw", name = "Raw")
two <- Heatmap(data_subset_norm, column_title = "Scaled", name = "Scaled")

one + two

Add annotations.

set.seed(123)
mat <- matrix(rnorm(100), 10)
rownames(mat) = paste0("R", 1:10)
colnames(mat) = paste0("C", 1:10)

column_ha = HeatmapAnnotation(
  foo1 = rep(c('N', 'T'), 5),
  bar1 = anno_barplot(colMeans(mat))
)

row_ha = rowAnnotation(
  foo2 = runif(10),
  bar2 = anno_barplot(rowMeans(mat))
)

Heatmap(mat, name = "mat", top_annotation = column_ha, right_annotation = row_ha)

Heatmap split.

Heatmap(mat, name = "mat", row_km = 3, column_km = 3)


sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] ComplexHeatmap_2.15.4 gridExtra_2.3         dendextend_1.17.1    
[4] pheatmap_1.0.12       workflowr_1.7.1      

loaded via a namespace (and not attached):
 [1] shape_1.4.6         circlize_0.4.15     gtable_0.3.4       
 [4] rjson_0.2.21        xfun_0.40           bslib_0.5.1        
 [7] ggplot2_3.4.4       GlobalOptions_0.1.2 processx_3.8.2     
[10] callr_3.7.3         vctrs_0.6.4         tools_4.3.2        
[13] ps_1.7.5            generics_0.1.3      stats4_4.3.2       
[16] parallel_4.3.2      tibble_3.2.1        fansi_1.0.5        
[19] cluster_2.1.4       pkgconfig_2.0.3     RColorBrewer_1.1-3 
[22] S4Vectors_0.40.1    lifecycle_1.0.3     compiler_4.3.2     
[25] stringr_1.5.0       git2r_0.32.0        munsell_0.5.0      
[28] getPass_0.2-2       codetools_0.2-19    clue_0.3-65        
[31] httpuv_1.6.12       htmltools_0.5.6.1   sass_0.4.7         
[34] yaml_2.3.7          later_1.3.1         pillar_1.9.0       
[37] crayon_1.5.2        jquerylib_0.1.4     whisker_0.4.1      
[40] cachem_1.0.8        iterators_1.0.14    viridis_0.6.4      
[43] foreach_1.5.2       tidyselect_1.2.0    digest_0.6.33      
[46] stringi_1.7.12      dplyr_1.1.3         rprojroot_2.0.3    
[49] fastmap_1.1.1       colorspace_2.1-0    cli_3.6.1          
[52] magrittr_2.0.3      utf8_1.2.4          scales_1.2.1       
[55] promises_1.2.1      rmarkdown_2.25      httr_1.4.7         
[58] matrixStats_1.0.0   png_0.1-8           GetoptLong_1.0.5   
[61] evaluate_0.22       knitr_1.44          IRanges_2.36.0     
[64] doParallel_1.0.17   viridisLite_0.4.2   rlang_1.1.1        
[67] Rcpp_1.0.11         glue_1.6.2          BiocGenerics_0.48.0
[70] rstudioapi_0.15.0   jsonlite_1.8.7      R6_2.5.1           
[73] fs_1.6.3