Using ggtree to Visualize Data on Tree‐Like Structures. Issue 1 (5th March 2020)
- Record Type:
- Journal Article
- Title:
- Using ggtree to Visualize Data on Tree‐Like Structures. Issue 1 (5th March 2020)
- Main Title:
- Using ggtree to Visualize Data on Tree‐Like Structures
- Authors:
- Yu, Guangchuang
- Editors:
- Baxevanis, Andreas D.
Petsko, Gregory A.
Stein, Lincoln D.
Stormo, Gary D. - Abstract:
- Abstract: Ggtree is an R/Bioconductor package for visualizing tree‐like structures and associated data. After 5 years of continual development, ggtree has been evolved as a package suite that contains treeio for tree data input and output, tidytree for tree data manipulation, and ggtree for tree data visualization. Ggtree was originally designed to work with phylogenetic trees, and has been expanded to support other tree‐like structures, which extends the application of ggtree to present tree data in other disciplines. This article contains five basic protocols describing how to visualize trees using the grammar of graphics syntax, how to visualize hierarchical clustering results with associated data, how to estimate bootstrap values and visualize the values on the tree, how to estimate continuous and discrete ancestral traits and visualize ancestral states on the tree, and how to visualize a multiple sequence alignment with a phylogenetic tree. The ggtree package is freely available at https://www.bioconductor.org/packages/ggtree . © 2020 by John Wiley & Sons, Inc. Basic Protocol 1 : Using grammar of graphics for visualizing trees Basic Protocol 2 : Visualizing hierarchical clustering using ggtree Basic Protocol 3 : Visualizing bootstrap values as symbolic points Basic Protocol 4 : Visualizing ancestral status Basic Protocol 5 : Visualizing a multiple sequence alignment with a phylogenetic tree
- Is Part Of:
- Current protocols in bioinformatics. Volume 69:Issue 1(2020)
- Journal:
- Current protocols in bioinformatics
- Issue:
- Volume 69:Issue 1(2020)
- Issue Display:
- Volume 69, Issue 1 (2020)
- Year:
- 2020
- Volume:
- 69
- Issue:
- 1
- Issue Sort Value:
- 2020-0069-0001-0000
- Page Start:
- n/a
- Page End:
- n/a
- Publication Date:
- 2020-03-05
- Subjects:
- grammar of graphics -- phylogeny -- tree associated data -- tree structure -- visualization
Bioinformatics -- Laboratory manuals
Nucleotide sequence -- Laboratory manuals
Amino acid sequence -- Laboratory manuals
Base Sequence
Amino Acid Sequence
Computational Biology -- methods
Databases, Genetic
Proteins -- analysis
Sequence Analysis -- methods
Sequence Homology
Amino acid sequence
Bioinformatics
Nucleotide sequence
Laboratory Manuals
Laboratory manuals
570.285 - Journal URLs:
- https://currentprotocols.onlinelibrary.wiley.com/journal/1934340x ↗
http://www3.interscience.wiley.com/cgi-bin/mrwhome/104554769/HOME ↗
http://onlinelibrary.wiley.com/ ↗ - DOI:
- 10.1002/cpbi.96 ↗
- Languages:
- English
- ISSNs:
- 1934-3396
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - BLDSS-3PM
British Library HMNTS - ELD Digital store - Ingest File:
- 13547.xml