library(ComplexHeatmap)
#> Loading required package: grid
#> ========================================
#> ComplexHeatmap version 2.24.0
#> 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
Compared with other packages
A simple heatmap.
bench::mark(
"heatmap()" = {
pdf(NULL)
heatmap(mat, Rowv = NA, Colv = NA)
dev.off()
NULL
},
"heatmap.2()" = {
pdf(NULL)
heatmap.2(mat, dendrogram = "none", trace = "none")
dev.off()
NULL
},
"Heatmap()" = {
pdf(NULL)
draw(Heatmap(mat,
cluster_rows = FALSE, cluster_columns = FALSE,
use_raster = TRUE
))
dev.off()
NULL
},
"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
}
)
#> 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() 150.59ms 150.71ms 4.37 138.85MB 4.37
#> 2 heatmap.2() 2.25s 2.25s 0.444 224.22MB 0.888
#> 3 Heatmap() 4.26s 4.26s 0.235 792.74MB 2.58
#> 4 pheatmap() 578.31ms 578.31ms 1.73 112.58MB 3.46
#> 5 ggalign() 1.73s 1.73s 0.579 2.48GB 10.4
For heatmap with dendrogram
bench::mark(
"heatmap()" = {
pdf(NULL)
heatmap(mat)
dev.off()
NULL
},
"heatmap.2()" = {
pdf(NULL)
heatmap.2(mat, trace = "none")
dev.off()
NULL
},
"Heatmap()" = {
pdf(NULL)
draw(Heatmap(mat,
row_dend_reorder = FALSE, column_dend_reorder = FALSE,
use_raster = TRUE
))
dev.off()
NULL
},
"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
}
)
#> 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() 3s 3s 0.333 173.72MB 2.33
#> 2 heatmap.2() 2.8s 2.8s 0.357 223.41MB 2.14
#> 3 Heatmap() 5.52s 5.52s 0.181 1.51GB 2.17
#> 4 pheatmap() 2.28s 2.28s 0.439 166.08MB 0.878
#> 5 ggalign() 4.67s 4.67s 0.214 2.55GB 4.71