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E-grāmata: Data Integration, Manipulation and Visualization of Phylogenetic Trees [Taylor & Francis e-book]

  • Formāts: 255 pages, 7 Tables, black and white; 109 Line drawings, black and white; 8 Halftones, black and white; 117 Illustrations, black and white
  • Sērija : Chapman & Hall/CRC Computational Biology Series
  • Izdošanas datums: 26-Aug-2022
  • Izdevniecība: Chapman & Hall/CRC
  • ISBN-13: 9781003279242
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  • Taylor & Francis e-book
  • Cena: 128,96 €*
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Data Integration, Manipulation and Visualization of Phylogenetic TreesPalielināt
  • Formāts: 255 pages, 7 Tables, black and white; 109 Line drawings, black and white; 8 Halftones, black and white; 117 Illustrations, black and white
  • Sērija : Chapman & Hall/CRC Computational Biology Series
  • Izdošanas datums: 26-Aug-2022
  • Izdevniecība: Chapman & Hall/CRC
  • ISBN-13: 9781003279242
Citas grāmatas par šo tēmu:
Taylor & Francis e-booksMore info about Taylor & Francis e-books
Rokasgrāmatas mājas lapa: https://www.taylorfrancis.com/books/9781003279242
Data Integration, Manipulation and Visualization of Phylogenetic Trees introduces and demonstrates data integration, manipulation and visualization of phylogenetic trees using a suite of R packages, tidytree, treeio, ggtree and ggtreeExtra. Using the most comprehensive packages for phylogenetic data integration and visualization, contains numerous examples that can be used for teaching and learning. Ideal for undergraduate readers and researchers with a working knowledge of R and ggplot2.

Key Features:





Manipulating phylogenetic tree with associated data using tidy verbs Integrating phylogenetic data from diverse sources Visualizing phylogenetic data using grammar of graphics
List of Figures
xi
List of Tables
xv
Preface xvii
Structure of the book xvii
Software information and conventions xviii
Acknowledgments xix
About the Author xxi
Part I Tree data input, output, and manipulation
1(70)
1 Importing Tree with Data
3(30)
1.1 Overview of Phylogenetic Tree Construction
3(2)
1.2 Phylogenetic Tree Formats
5(8)
1.2.1 Newick tree format
5(1)
1.2.2 NEXUS tree format
6(2)
1.2.3 New Hampshire eXtended format
8(1)
1.2.4 Jplace format
8(1)
1.2.5 Software outputs
9(4)
1.3 Getting Tree Data with treeio
13(18)
1.3.1 Overview of treeio
15(2)
1.3.2 Function demonstration
17(10)
1.3.3 Converting other tree-like objects to phylo or treedata objects
27(1)
1.3.4 Getting information from treedata object
28(3)
1.4 Summary
31(2)
2 Manipulating Tree with Data
33(26)
2.1 Manipulating Tree Data Using Tidy Interface
33(4)
2.1.1 The phylo object
33(2)
2.1.2 The treedata object
35(1)
2.1.3 Access related nodes
36(1)
2.2 Data Integration
37(8)
2.2.1 Combining tree data
37(4)
2.2.2 Linking external data to phylogeny
41(2)
2.2.3 Grouping taxa
43(2)
2.3 Rerooting tree
45(4)
2.4 Rescaling Tree Branches
49(1)
2.5 Subsetting Tree with Data
50(3)
2.5.1 Removing tips in a phylogenetic tree
50(1)
2.5.2 Subsetting tree by tip label
50(3)
2.5.3 Subsetting tree by internal node number
53(1)
2.6 Manipulating Tree Data for Visualization
53(4)
2.7 Summary
57(2)
3 Exporting Tree with Data
59(12)
3.1 Introduction
59(1)
3.2 Exporting Tree Data to BEAST Nexus Format
60(6)
3.2.1 Exporting/converting software output
60(1)
3.2.2 Combining tree with external data
61(3)
3.2.3 Merging tree data from different sources
64(2)
3.3 Exporting Tree Data to the jtree Format
66(3)
3.4 Summary
69(2)
Part II Tree data visualization and annotation
71(88)
4 Phylogenetic Tree Visualization
73(24)
4.1 Introduction
73(1)
4.2 Visualizing Phylogenetic Tree with ggtree
74(8)
4.2.1 Basic Tree Visualization
75(1)
4.2.2 Layouts of a phylogenetic tree
76(6)
4.3 Displaying Tree Components
82(10)
4.3.1 Displaying treescale (evolution distance)
82(1)
4.3.2 Displaying nodes/tips
82(1)
4.3.3 Displaying labels
83(2)
4.3.4 Displaying root-edge
85(1)
4.3.5 Color tree
85(3)
4.3.6 Rescale tree
88(3)
4.3.7 Modify components of a theme
91(1)
4.4 Visualize a List of Trees
92(3)
4.4.1 Annotate one tree with values from different variables
94(1)
4.4.2 DensiTree
95(1)
4.5 Summary
95(2)
5 Phylogenetic Tree Annotation
97(14)
5.1 Visualizing and Annotating Tree Using Grammar of Graphics
97(1)
5.2 Layers for Tree Annotation
98(9)
5.2.1 Colored strips
98(5)
5.2.2 Highlight clades
103(1)
5.2.3 Taxa connection
104(2)
5.2.4 Uncertainty of evolutionary inference
106(1)
5.3 Tree Annotation with Output from Evolution Software
107(3)
5.3.1 Tree annotation using data from evolutionary analysis software
107(3)
5.4 Summary
110(1)
6 Visual Exploration of Phylogenetic Trees
111(12)
6.1 Viewing Selected Clade
112(1)
6.2 Scaling Selected Clade
113(1)
6.3 Collapsing and Expanding Clade
114(2)
6.4 Grouping Taxa
116(1)
6.5 Exploring Tree Structure
117(4)
6.6 Summary
121(2)
7 Plotting Tree with Data
123(12)
7.1 Mapping Data to The tree Structure
123(1)
7.2 Aligning Graph to the Tree Based on the Tree Structure
124(2)
7.3 Visualize a Tree with an Associated Matrix
126(4)
7.3.1 Visualize a tree with multiple associated matrices
129(1)
7.4 Visualize a Tree with Multiple Sequence Alignments
130(1)
7.5 Composite Plots
131(2)
7.6 Summary
133(2)
8 Annotating Tree with Silhouette Images and Sub-plots
135(12)
8.1 Annotating Tree with Images
135(1)
8.2 Annotating Tree with Phylopic
136(1)
8.3 Annotating Tree with Sub-plots
137(2)
8.3.1 Annotate with bar charts
138(1)
8.3.2 Annotate with pie charts
138(1)
8.3.3 Annotate with mixed types of charts
139(1)
8.4 Have Fun with Phylomoji
139(6)
8.4.1 Emoji in circular/fan layout tree
141(1)
8.4.2 Emoji to label clades
142(2)
8.4.3 Apple Color Emoji
144(1)
8.4.4 Phylomoji in ASCII art
145(1)
8.5 Summary
145(2)
9 Ggtree for Other Tree-like Objects
147(12)
9.1 Ggtree for Phylogenetic Tree Objects
147(6)
9.1.1 The phylo4 and phylo4d objects
147(1)
9.1.2 The phylog object
148(2)
9.1.3 The phyloseq object
150(3)
9.2 Ggtree for Dendrograms
153(1)
9.3 Ggtree for Tree Graph
154(1)
9.4 Ggtree for Other Tree-like Structures
155(3)
9.5 Summary
158(1)
Part III Ggtree extensions
159(22)
10 Ggtree Extra for Presenting Data on a Circular Layout
161(16)
10.1 Introduction
161(1)
10.2 Aligning Graphs to the Tree Based on a Tree Structure
161(2)
10.3 Aligning Multiple Graphs to the Tree for Multi-dimensional Data
163(4)
10.4 Examples for Population Genetics
167(8)
10.5 Summary
175(2)
11 Other ggtree Extensions
177(4)
11.1 Taxonomy Annotation Using MicrobiotaProcess
177(2)
11.2 Visualizing Phylogenetic Network Using Tanggle
179(1)
11.3 Summary
180(1)
Part IV Miscellaneous topics
181(28)
12 Ggtree Utilities
183(14)
12.1 Facet Utilities
183(2)
12.1.1 Facet widths
183(2)
12.1.2 facet__labeller
185(1)
12.2 Geometric Layers
185(2)
12.3 Layout Utilities
187(1)
12.4 Scale Utilities
188(2)
12.4.1 Expand x limit for a specific facet panel
188(1)
12.4.2 Expand plot limit by the ratio of plot range
189(1)
12.5 Tree data utilities
190(2)
12.5.1 Filter tree data
190(1)
12.5.2 Flatten list-column tree data
191(1)
12.6 Tree Utilities
192(4)
12.6.1 Extract tip order
192(2)
12.6.2 Padding taxa labels
194(2)
12.7 Interactive ggtree Annotation
196(1)
13 Gallery of Reproducible Examples
197(12)
13.1 Visualizing pairwise nucleotide sequence distance with a phylogenetic tree
197(3)
13.2 Displaying Different Symbolic Points for Bootstrap Values
200(2)
13.3 Highlighting Different Groups
202(3)
13.4 Phylogenetic Tree with Genome Locus Structure
205(4)
A Frequently Asked Questions
209(20)
A.1 Installation
209(1)
A.2 Basic R Related
210(1)
A.2.1 Use your local file
210(1)
A.3 Aesthetic, mapping
210(1)
A.3.1 Inherit aesthetic mapping
210(1)
A.3.2 Never use $ in aesthetic mapping
211(1)
A.4 Text and Label
211(5)
A.4.1 Tip label truncated
211(1)
A.4.2 Modify (tip) labels
212(1)
A.4.3 Formatting (tip) labels
213(2)
A.4.4 Avoid overlapping text labels
215(1)
A.4.5 Bootstrap values from Newick format
215(1)
A.5 Branch Setting
216(7)
A.5.1 Plot the same tree as in plot.phylo()
216(1)
A.5.2 Specifying the order of the tips
217(1)
A.5.3 Shrink outlier long branch
218(1)
A.5.4 Attach a new tip to a tree
219(2)
A.5.5 Change colors or line types of arbitrarily selected branches
221(1)
A.5.6 Add an arbitrary point to a branch
222(1)
A.6 Different X-axis Labels for Different Facet Panels
223(1)
A.7 Plot Something behind the Phylogeny
223(1)
A.8 Enlarge Center Space in Circular/Fan Layout Tree
224(1)
A.9 Use the Most Distant Tip from the Root as the Origin of the Timescale
225(1)
A.10 Remove Blank Margins for Circular Layout Tree
225(3)
A.11 Edit Tree Graphic Details
228(1)
B Related Tools
229(10)
B.1 MicrobiotaProcess: Convert Taxonomy Table to a treedata Object
229(1)
B.2 rtol: An R Interface to Open Tree API
230(1)
B.3 Print ASCII-art Rooted Tree
231(3)
B.4 Zoom in on the Selected Portion
234(1)
B.5 Tips for Using ggtree with ggimage
234(2)
B.5.1 Example 1: Remove background of images
235(1)
B.5.2 Example 2: Plot tree on a background image
235(1)
B.6 Run ggtree in Jupyter Notebook
236(3)
Figures and Tables 239(4)
Publications of the ggtree Package Suite 243(2)
References 245(8)
Index 253
Guangchuang Yu is a professor of bioinformatics, director of the Department of Bioinformatics, Southern Medical University. He earned his Ph.D. from the School of Public Health, The University of Hong Kong. As an active R user, he has authored several R packages and has supervised post-graduate students to develop a few other packages, including ggmsa, ggtreeExtra, MicrobiomeProfiler and MicrobiotaProcess.
Permanent link: https://www.kriso.lv/db/9781003279242_pe.html
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