Package: ggtreeExtra 1.15.0

Shuangbin Xu

ggtreeExtra: An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.

Authors:Shuangbin Xu [aut, cre], Guangchuang Yu [aut, ctb]

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ggtreeExtra.pdf |ggtreeExtra.html✨
ggtreeExtra/json (API)
NEWS

# Install 'ggtreeExtra' in R:

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

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

On BioConductor:ggtreeExtra-1.15.0(bioc 3.20)ggtreeExtra-1.14.0(bioc 3.19)

bioconductor-package

18 exports 1.16 score 55 dependencies 1 dependents 2 mentions

Last updated 2 months agofrom:eb59d964d1

Exports:%>%fruit_plot geom_fruit geom_fruit_list ggplot_add position_dodgex position_dodgex2 position_identityx position_jitterdodgex position_jitterx position_points_jitterx position_points_sinax position_raincloudx position_stackx PositionJitterdodgex PositionJitterx td_filter td_unnest

Dependencies:ape aplot cachem cli colorspace cpp11 digest dplyr fansi farver fastmap fs generics ggfun ggnewscale ggplot2 ggplotify ggtree glue gridGraphics gtable isoband jsonlite labeling lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv munsell nlme patchwork pillar pkgconfig purrr R6 RColorBrewer Rcpp rlang scales stringi stringr tibble tidyr tidyselect tidytree treeio utf8 vctrs viridisLite withr yulab.utils

ggtreeExtra

| Shuangbin Xu and GuangChuang Yu | School of Basic Medical Sciences, Southern Medical University

Rendered fromggtreeExtra.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-07-07
Started: 2020-07-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
plot tree with associated data in another method.	fruit_plot geom_fruit
geom_fruit_list	geom_fruit_list
Dodge overlapping objects side-to-side which can be shifted verically or horizontally.	position_dodgex position_dodgex2
adjust identity position which can be shifted vertically or horizontally.	position_identityx
Simultaneously dodge and jitter, and the whole layer can be shifted vertically or horizontally	position_jitterdodgex
Jitter points to avoid overplotting, and the whole points can be shifted vertically or horizontally	position_jitterx
Randomly jitter the points in a ridgeline plot which can be shifted horizontally	position_points_jitterx
adjust ridgeline plot position which can be shifted vertically or horizontally.	position_points_sinax
Create a cloud of randomly jittered points below a ridgeline plot which can be shifted horizontally	position_raincloudx
Stack overlapping objects which can be shifted vertically or horizontally	position_stackx
PositionDodgex	PositionDodgex PositionDodgex2 PositionIdentityx PositionPointsJitterx PositionPointsSinax PositionRaincloudx PositionStackx
PositionJitterdodgex	PositionJitterdodgex
PositionJitterx	PositionJitterx