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
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() 146.28ms 308.12ms 3.25 NA 3.25
#> 2 gplots::heatmap.2() 2.33s 2.33s 0.428 NA 0.428
#> 3 ComplexHeatmap::Heatmap() 4.8s 4.8s 0.208 NA 1.67
#> 4 pheatmap::pheatmap() 588.54ms 588.54ms 1.70 NA 3.40
#> 5 ggalign() 2.05s 2.05s 0.489 NA 7.82
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() 2.66s 2.66s 0.376 NA 1.13
#> 2 gplots::heatmap.2() 2.78s 2.78s 0.359 NA 1.08
#> 3 ComplexHeatmap::Heatmap() 5.82s 5.82s 0.172 NA 1.20
#> 4 pheatmap::pheatmap() 2.2s 2.2s 0.454 NA 0
#> 5 ggalign() 4.41s 4.41s 0.227 NA 3.85