Benchmarks

library(ComplexHeatmap)
#> Loading required package: grid
#> ========================================
#> ComplexHeatmap version 2.24.1
#> Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
#> Github page: https://github.com/jokergoo/ComplexHeatmap
#> Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
#> 
#> If you use it in published research, please cite either one:
#> - Gu, Z. Complex Heatmap Visualization. iMeta 2022.
#> - Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
#>     genomic data. Bioinformatics 2016.
#> 
#> 
#> The new InteractiveComplexHeatmap package can directly export static 
#> complex heatmaps into an interactive Shiny app with zero effort. Have a try!
#> 
#> This message can be suppressed by:
#>   suppressPackageStartupMessages(library(ComplexHeatmap))
#> ========================================
library(pheatmap)
#> 
#> Attaching package: 'pheatmap'
#> The following object is masked from 'package:ComplexHeatmap':
#> 
#>     pheatmap
library(gplots)
#> 
#> Attaching package: 'gplots'
#> The following object is masked from 'package:stats':
#> 
#>     lowess
library(ggalign)
#> Loading required package: ggplot2
#> 
#> Attaching package: 'ggalign'
#> The following object is masked from 'package:ggplot2':
#> 
#>     element_polygon

set.seed(123)
n <- 1000
mat <- matrix(rnorm(n * n), nrow = n)

Compared with other packages

A simple heatmap.

bench::mark(
    "heatmap()" = {
        pdf(NULL)
        heatmap(mat, Rowv = NA, Colv = NA)
        dev.off()
        NULL
    },
    "gplots::heatmap.2()" = {
        pdf(NULL)
        heatmap.2(mat, dendrogram = "none", trace = "none")
        dev.off()
        NULL
    },
    "ComplexHeatmap::Heatmap()" = {
        pdf(NULL)
        draw(Heatmap(mat,
            cluster_rows = FALSE, cluster_columns = FALSE,
            use_raster = TRUE
        ))
        dev.off()
        NULL
    },
    "pheatmap::pheatmap()" = {
        pdf(NULL)
        pheatmap(mat, cluster_rows = FALSE, cluster_cols = FALSE)
        dev.off()
        NULL
    },
    "ggalign()" = {
        pdf(NULL)
        print(ggheatmap(mat, filling = "raster"))
        dev.off()
        NULL
    },
    memory = FALSE
)
#> Warning: Some expressions had a GC in every iteration; so filtering is
#> disabled.
#> # A tibble: 5 × 6
#>   expression                     min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr>                <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 heatmap()                 149.86ms 150.36ms     6.59         NA     6.59
#> 2 gplots::heatmap.2()          2.35s    2.35s     0.426        NA     1.70
#> 3 ComplexHeatmap::Heatmap()    5.39s    5.39s     0.186        NA     1.67
#> 4 pheatmap::pheatmap()      556.19ms 556.19ms     1.80         NA     0   
#> 5 ggalign()                    1.79s    1.79s     0.559        NA     8.94

For heatmap with dendrogram

bench::mark(
    "heatmap()" = {
        pdf(NULL)
        heatmap(mat)
        dev.off()
        NULL
    },
    "gplots::heatmap.2()" = {
        pdf(NULL)
        heatmap.2(mat, trace = "none")
        dev.off()
        NULL
    },
    "ComplexHeatmap::Heatmap()" = {
        pdf(NULL)
        draw(Heatmap(mat,
            row_dend_reorder = FALSE, column_dend_reorder = FALSE,
            use_raster = TRUE
        ))
        dev.off()
        NULL
    },
    "pheatmap::pheatmap()" = {
        pdf(NULL)
        pheatmap(mat)
        dev.off()
        NULL
    },
    "ggalign()" = {
        pdf(NULL)
        print(ggheatmap(mat, filling = "raster") +
            anno_top() + align_dendro() +
            anno_right() + align_dendro())
        dev.off()
        NULL
    },
    memory = FALSE
)
#> Warning: Some expressions had a GC in every iteration; so filtering is
#> disabled.
#> # A tibble: 5 × 6
#>   expression                     min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr>                <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 heatmap()                    2.68s    2.68s     0.374        NA    1.87 
#> 2 gplots::heatmap.2()          3.18s    3.18s     0.315        NA    1.26 
#> 3 ComplexHeatmap::Heatmap()    5.45s    5.45s     0.184        NA    1.28 
#> 4 pheatmap::pheatmap()          2.2s     2.2s     0.455        NA    0.455
#> 5 ggalign()                    4.81s    4.81s     0.208        NA    3.74