Difference between revisions of "Ggtree"
From EEBedia
Kevin Keegan (Talk | contribs) (Created page with "{| border="0" |- |rowspan="2" valign="top"|200px |<span style="font-size: x-large">[http://phylogeny.uconn.edu/courses/ EEB 5349: Phylogenetics]</span>...") |
Kevin Keegan (Talk | contribs) |
||
| Line 13: | Line 13: | ||
== Introduction == | == Introduction == | ||
| + | |||
| + | == Getting Started == | ||
| + | |||
| + | Download the tree file (Paul can you host the treefile?) and install the packages we will be using. We'll be using the packages: | ||
| + | |||
| + | BiocInstaller | ||
| + | ape | ||
| + | Biostrings | ||
| + | ggplot2 | ||
| + | ggtree | ||
| + | phytools | ||
| + | ggrepel | ||
| + | stringr | ||
| + | stringi | ||
| + | abind | ||
| + | |||
| + | You can install a package like so: | ||
| + | |||
| + | install.packages("BiocInstaller") | ||
| + | |||
| + | |||
| + | |||
== References == | == References == | ||
Yu G, Smith D, Zhu H, Guan Y and Lam TT (2017). “ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.” Methods in Ecology and Evolution, 8, pp. 28-36. doi: 10.1111/2041-210X.12628, http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract. | Yu G, Smith D, Zhu H, Guan Y and Lam TT (2017). “ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.” Methods in Ecology and Evolution, 8, pp. 28-36. doi: 10.1111/2041-210X.12628, http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract. | ||
Revision as of 15:24, 7 March 2018
|
EEB 5349: Phylogenetics |
by Kevin Keegan
Goals
To introduce you to the R package ggtree for plotting phylogenetic trees.
Introduction
Getting Started
Download the tree file (Paul can you host the treefile?) and install the packages we will be using. We'll be using the packages:
BiocInstaller ape Biostrings ggplot2 ggtree phytools ggrepel stringr stringi abind
You can install a package like so:
install.packages("BiocInstaller")
References
Yu G, Smith D, Zhu H, Guan Y and Lam TT (2017). “ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.” Methods in Ecology and Evolution, 8, pp. 28-36. doi: 10.1111/2041-210X.12628, http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract.
