Package: ggtreeSpace 1.9.0

Guangchuang Yu

ggtreeSpace: Visualizing Phylomorphospaces using 'ggtree'

This package is a comprehensive visualization tool specifically designed for exploring phylomorphospace. It not only simplifies the process of generating phylomorphospace, but also enhances it with the capability to add graphic layers to the plot with grammar of graphics to create fully annotated phylomorphospaces. It also provide some utilities to help interpret evolutionary patterns.

Authors:Guangchuang Yu [aut, cre, ths, cph], Li Lin [ctb]

ggtreeSpace_1.9.0.tar.gz
ggtreeSpace_1.9.0.zip(r-4.7)ggtreeSpace_1.9.0.zip(r-4.6)ggtreeSpace_1.9.0.zip(r-4.5)
ggtreeSpace_1.9.0.tgz(r-4.6-any)ggtreeSpace_1.9.0.tgz(r-4.5-any)
ggtreeSpace_1.9.0.tar.gz(r-4.7-any)ggtreeSpace_1.9.0.tar.gz(r-4.6-any)
ggtreeSpace_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggtreeSpace/json (API)

# Install 'ggtreeSpace' in R:

install.packages('ggtreeSpace', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yulab-smu/ggtreespace/issues

On BioConductor:ggtreeSpace-1.9.0(bioc 3.24)ggtreeSpace-1.8.0(bioc 3.23)

annotation visualization phylogenetics software

5.32 score 5 stars 14 scripts 234 downloads 8 exports 102 dependencies

Last updated from:c97e28dda2. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	150
linux-devel-x86_64	WARNING	249
source / vignettes	OK	230
linux-release-x86_64	WARNING	252
macos-release-arm64	WARNING	130
macos-oldrel-arm64	WARNING	191
windows-devel	WARNING	138
windows-release	WARNING	149
windows-oldrel	WARNING	128
wasm-release	OK	142

Exports:geom_treespace geom_tsheatmap ggplot_add ggtreespace make_ts_data phylospm theme_treespace theme_treespace2

Dependencies:ape aplot base64enc bslib cachem cli clusterGeneration coda codetools combinat cpp11 crayon deldir DEoptim digest doParallel dplyr evaluate expm farver fastmap fastmatch fontawesome fontBitstreamVera fontLiberation fontquiver forcats foreach fs gdtools generics GGally ggfun ggiraph ggplot2 ggplotify ggstats ggtree glue gridGraphics gtable highr hms htmltools htmlwidgets igraph interp isoband iterators jquerylib jsonlite knitr labeling lattice lazyeval lifecycle magrittr maps MASS Matrix memoise mime mnormt nlme numDeriv optimParallel patchwork phangorn phytools pillar pkgconfig prettyunits progress purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppEigen rlang rmarkdown S7 sass scales scatterplot3d stringi stringr systemfonts tibble tidyr tidyselect tidytree tinytex treeio utf8 vctrs viridisLite withr xfun yaml yulab.utils

ggtreeSpace-Getting Started

Introduction | Installation | Demonstration | Session information

Rendered fromggtreeSpace.Rmdusingknitr::rmarkdown

Last update: 2024-04-13
Started: 2024-03-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A layer of phylomorphospace	geom_treespace
Add a layer of heat map with trait data	geom_tsheatmap
Plot phylomorphospace	ggtreespace
Make plot data for ggtreespace. This function processes a phylogenetic tree and associated trait data to create a data frame suitable for plotting with `ggtreespace`.	make_ts_data
Plot phylogenetic scatterplot matrix.	phylospm
Phylomorphospace theme No.1, with arrow-end axis and grey panel grid.	theme_treespace
Phylomorphospace theme No.2, with blank background and panel border.	theme_treespace2