library(ComplexHeatmap)
#> Loading required package: grid
#> ========================================
#> ComplexHeatmap version 2.22.0
#> 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: ggplot2A 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
}
)
#> 'magick' package is suggested to install to give better rasterization.
#>
#> Set `ht_opt$message = FALSE` to turn off this message.
#> 'magick' package is suggested to install to give better rasterization.
#>
#> Set `ht_opt$message = FALSE` to turn off this message.
#> 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() 152.86ms 154.24ms 6.36 139.11MB 6.36
#> 2 heatmap.2() 2.23s 2.23s 0.448 224.23MB 1.34
#> 3 Heatmap() 4.36s 4.36s 0.229 805.38MB 3.44
#> 4 pheatmap() 649.02ms 649.02ms 1.54 124.1MB 0
#> 5 ggalign() 1.64s 1.64s 0.609 2.51GB 10.3For 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
}
)
#> 'magick' package is suggested to install to give better rasterization.
#>
#> Set `ht_opt$message = FALSE` to turn off this message.
#> 'magick' package is suggested to install to give better rasterization.
#>
#> Set `ht_opt$message = FALSE` to turn off this message.
#> 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() 2.65s 2.65s 0.378 173.72MB 2.64
#> 2 heatmap.2() 2.77s 2.77s 0.362 223.41MB 2.53
#> 3 Heatmap() 5.35s 5.35s 0.187 1.53GB 2.62
#> 4 pheatmap() 2.27s 2.27s 0.441 177.53MB 0.882
#> 5 ggalign() 5.13s 5.13s 0.195 2.58GB 4.68