Introduction
ggtreeSpace is a comprehensive visualization tool design to plot phylomorphospace with the grammar of graphics.
Function
You can plot phylomorphospace easily with ggtreeSpace fuction:
suppressPackageStartupMessages(library(ggtree))
suppressPackageStartupMessages(library(ggtreeSpace))
suppressPackageStartupMessages(library(phytools))
tr <- rtree(15)
td <- fastBM(tr, nsim = 2)
ggtreeSpace(tr, td) +
geom_tippoint()
ggtreeSpace supports adding phylomorphospace as a graphic layer.
suppressPackageStartupMessages(library(ggtree))
suppressPackageStartupMessages(library(ggtreeSpace))
suppressPackageStartupMessages(library(phytools))
suppressPackageStartupMessages(library(ggplot2))
tr1 <- rtree(15)
td1 <- fastBM(tr1, nsim = 2)
ggplot() +
geom_treeSpace(tr1, td1)
You can add an additional layer of heatmap base on your data.
suppressPackageStartupMessages(library(ggtree))
suppressPackageStartupMessages(library(ggtreeSpace))
suppressPackageStartupMessages(library(phytools))
tr2 <- rtree(15)
td2 <- fastBM(tr2, nsim = 2, bounds = c(0, Inf))
tdex2 <- data.frame(z = fastBM(tr2, nsim = 1),
node = 1:15)
p <- ggtreeSpace(tr2, td2)
p %<+% tdex2 +
geom_tippoint() +
geom_tsheatmap(trait = "z", alpha = 0.7 ,resolution = 0.01, bin = 12)
Session information
Here is the output of sessionInfo() on the system on which this document was compiled:
## R Under development (unstable) (2024-03-18 r86148)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggplot2_3.5.0 phytools_2.1-1 maps_3.4.2 ape_5.7-1
## [5] ggtreeSpace_0.99.0 ggtree_3.11.1
##
## loaded via a namespace (and not attached):
## [1] fastmatch_1.1-4 gtable_0.3.4 xfun_0.42
## [4] bslib_0.6.2 lattice_0.22-6 numDeriv_2016.8-1.1
## [7] quadprog_1.5-8 vctrs_0.6.5 tools_4.4.0
## [10] generics_0.1.3 yulab.utils_0.1.4 parallel_4.4.0
## [13] tibble_3.2.1 fansi_1.0.6 highr_0.10
## [16] pkgconfig_2.0.3 Matrix_1.7-0 ggplotify_0.1.2
## [19] scatterplot3d_0.3-44 lifecycle_1.0.4 farver_2.1.1
## [22] compiler_4.4.0 treeio_1.27.0 prettydoc_0.4.1
## [25] munsell_0.5.0 mnormt_2.1.1 combinat_0.0-8
## [28] akima_0.6-3.4 codetools_0.2-19 ggfun_0.1.4
## [31] htmltools_0.5.7 sass_0.4.9 yaml_2.3.8
## [34] lazyeval_0.2.2 pillar_1.9.0 jquerylib_0.1.4
## [37] tidyr_1.3.1 MASS_7.3-60.2 cachem_1.0.8
## [40] clusterGeneration_1.3.8 iterators_1.0.14 foreach_1.5.2
## [43] nlme_3.1-164 phangorn_2.11.1 tidyselect_1.2.1
## [46] aplot_0.2.2 digest_0.6.35 dplyr_1.1.4
## [49] purrr_1.0.2 labeling_0.4.3 fastmap_1.1.1
## [52] grid_4.4.0 colorspace_2.1-0 expm_0.999-9
## [55] cli_3.6.2 magrittr_2.0.3 patchwork_1.2.0
## [58] optimParallel_1.0-2 utf8_1.2.4 withr_3.0.0
## [61] scales_1.3.0 sp_2.1-3 rmarkdown_2.26
## [64] igraph_2.0.3 memoise_2.0.1 coda_0.19-4.1
## [67] evaluate_0.23 knitr_1.45 doParallel_1.0.17
## [70] viridisLite_0.4.2 gridGraphics_0.5-1 rlang_1.1.3
## [73] isoband_0.2.7 Rcpp_1.0.12 glue_1.7.0
## [76] tidytree_0.4.6 jsonlite_1.8.8 R6_2.5.1
## [79] fs_1.6.3