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() 153.74ms 153.76ms 5.59 139.11MB 7.46
#> 2 heatmap.2() 2.49s 2.49s 0.401 224.23MB 1.61
#> 3 Heatmap() 4.1s 4.1s 0.244 805.38MB 2.93
#> 4 pheatmap() 628.63ms 628.63ms 1.59 124.1MB 1.59
#> 5 ggalign() 2.13s 2.13s 0.470 2.51GB 11.8For 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() 2.92s 2.92s 0.343 173.72MB 2.06
#> 2 heatmap.2() 2.73s 2.73s 0.367 223.41MB 2.20
#> 3 Heatmap() 5.23s 5.23s 0.191 1.53GB 2.10
#> 4 pheatmap() 2.24s 2.24s 0.447 177.53MB 0.894
#> 5 ggalign() 4.64s 4.64s 0.216 2.58GB 4.74