Title: Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574)
Version: 0.0.6
Description: The companion package that provides all the datasets used in the book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574).
Depends: R (≥ 3.5)
License: Artistic-2.0
Encoding: UTF-8
URL: https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/
BugReports: https://github.com/YuLab-SMU/TDbook/issues
LazyData: true
RoxygenNote: 7.2.1
NeedsCompilation: no
Packaged: 2022-08-13 09:39:17 UTC; ygc
Author: Guangchuang Yu ORCID iD [aut, cre, cph], Shuangbin Xu ORCID iD [aut], Lin Li ORCID iD [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Repository: CRAN
Date/Publication: 2022-08-13 11:20:02 UTC

TDbook: Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574)

Description

The companion package that provides all the datasets used in the book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574).

https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/

Author(s)

Maintainer: Guangchuang Yu guangchuangyu@gmail.com (ORCID) [copyright holder]

Authors:

See Also

Useful links:

Data set containing multiple sequence alignment information

Description

This data set contains multiple sequence alignment information to be attached to the tree.
Chap.7.4

Format

AAbin

Examples

data(AA_sequence)

Population genetics data No.1

Description

Population genetics data to be visualized using multiple graphs and attached to tree No.1 with geo_fruit() of ggtreeExtra.
Chap.10.4

Format

A data frame contains 305 rows and 20 variables, with a column of "node" or first column of taxa labels.

References

Chow, Nancy A., José F. Muñoz, Lalitha Gade, Elizabeth L. Berkow, Xiao Li, Rory M. Welsh, Kaitlin Forsberg, et al. Tracing the Evolutionary History and Global Expansion of Candida Auris Using Population Genomic Analyses. Edited by Geraldine Butler and Kirsten Nielsen. mBio, Volume 11, Issue 2, April 2020. doi:10.1128/mBio.03364-19

Examples

data(df_Candidaauris_data)

Population genetics data No.2

Description

Population genetics data to be visualized using multiple graphs and attached to tree No.2 with geo_fruit() of ggtreeExtra.
Chap.10.4

Format

A data frame contains 1351 rows and 7 variables, with a column of "node" or first column of taxa labels.

References

Wong, Vanessa K., Stephen Baker, Derek J. Pickard, Julian Parkhill, Andrew J. Page, Nicholas A. Feasey, Robert A. Kingsley, et al. Phylogeographical Analysis of the Dominant Multidrug-Resistant H58 Clade of Salmonella Typhi Identifies Inter- and Intracontinental Transmission Events. Nature Genetics, Volume 47, Issue 6, May 2015, Pages 632–39. doi:10.1038/ng.3281

Examples

data(df_NJIDqgsS)

Allele table

Description

The allele table with original data to be processed to SNP data. Then attached to the tree after visualizing.
Chap.7.2

Format

A data frame contains 386 rows and 385 variables, with first row of tips labels.

Source

https://raw.githubusercontent.com/katholt/plotTree/master/tree_example_april2015/alleles.csv

Examples

data(df_alleles)

Data frame containing hierarchical relationship

Description

This Data frame contains hierarchical relationship to be visualized with another data frame that contains taxa and factor information and pvalue, using ggdiffcalde() of The MicrobiotaProcess package.
It's the analysis result of diff_analysis() using public datasets (Kostic et al. 2012) with The MicrobiotaProcess package.
These data frame are used to demonstrates how to visualize the differential taxonomy tree with The MicrobiotaProcess package.
Chap.11.1

Format

A data frame to store taxonomy information, contains 1351 rows and 7 variables (classification levels).

References

Kostic, Aleksandar D, Dirk Gevers, Chandra Sekhar Pedamallu, Monia Michaud, Fujiko Duke, Ashlee M Earl, Akinyemi I Ojesina, et al. Genomic Analysis Identifies Association of Fusobacterium with Colorectal Carcinoma.” Genome Research, Volume 22, Issue 2, 2012, Pages 292–98. doi:10.1101/gr.126573.111

Examples

data(df_alltax_info)

Trait data

Description

The trait data to be visualized with bar plot and attached to the tree.
Chap.7.2

Format

A data frame contains 386 rows and 2 variables, with a column of "node" or first column of taxa labels.

Source

https://raw.githubusercontent.com/katholt/plotTree/master/tree_example_april2015/bar.csv

Examples

data(df_bar_data)

Data set of the abundance of microbes at the body sites of greatest prevalence

Description

The data set of abundance of microbes at the body sites of greatest prevalence to be visualized using barplot and attached to the tree.
Chap.10.3

Format

A data frame contains 332 rows and 3 variables, with a column of "node" or first column of taxa labels.

References

Asnicar, Francesco, George Weingart, Timothy L Tickle, Curtis Huttenhower, and Nicola Segata. Compact Graphical Representation of Phylogenetic Data and Metadata with GraPhlAn. PeerJ, 3: e1029, June 2015. doi:10.7717/peerj.1029

Examples

data(df_barplot_attr)

Data frame containing taxa and factor information and pvalue

Description

This Data frame contains taxa and factor information and pvalue to be visualized with another data frame that contains hierarchical relationship, using ggdiffcalde() of The MicrobiotaProcess package.
These data frame are used to demonstrates how to visualize the differential taxonomy tree with The MicrobiotaProcess package.
Chap.11.1

Format

A data frame contains 36 rows and 3 variables.

References

Kostic, Aleksandar D, Dirk Gevers, Chandra Sekhar Pedamallu, Monia Michaud, Fujiko Duke, Ashlee M Earl, Akinyemi I Ojesina, et al. Genomic Analysis Identifies Association of Fusobacterium with Colorectal Carcinoma.” Genome Research, Volume 22, Issue 2, 2012, Pages 292–98. doi:10.1101/gr.126573.111

Examples

data(df_difftax)

Sampling information data set

Description

The sampling information data set be attached to the tree tip.
Chap.7.2

Format

A data frame contains 386 rows and 6 variables, with a column of "node" or first column of taxa labels.

Source

https://raw.githubusercontent.com/katholt/plotTree/master/tree_example_april2015/info.csv

Examples

data(df_info)

Nodedata to be mapped to tree

Description

This data contains annotation information about nodes of "tree_boots.nwk", that is to be mapped to the tree using the ⁠%<+%⁠ operator.
Chap.7.1

Format

A data frame with 6 rows and 6 variables with a column of node or first column of taxa labels.

Source

https://raw.githubusercontent.com/TreeViz/metastyle/master/design/viz_targets_exercise/inode_data.csv

Examples

data(df_inode_data)

Data set of the abundance and types of microbes

Description

The data set of abundance of microbes at different body sites to be visualized using heatmap and attached to the tree.
Chap.10.3

Format

A data frame contains 2324 rows and 3 variables, with a column of "node" or first column of taxa labels.

References

Asnicar, Francesco, George Weingart, Timothy L Tickle, Curtis Huttenhower, and Nicola Segata. Compact Graphical Representation of Phylogenetic Data and Metadata with GraPhlAn. PeerJ, 3: e1029, June 2015. doi:10.7717/peerj.1029

Examples

data(df_ring_heatmap)

Data frame containing slv information

Description

Data frame containing slv information to scale the color of the tree using the continuous parameter of ggtree to plot continuous state transition in edges.
Chap.4.3.5. This file is provided in http://www.phytools.org/eqg2015/asr.html.

Format

A data frame contains 100 rows and 1 variables.

Source

http://www.phytools.org/eqg2015/data/svl.csv

Examples

data(df_svl)

Tipdata to be mapped to tree

Description

This data contains annotation information about tips of tree_boots, that is to be mapped to the tree using the ⁠%<+%⁠ operator.
Chap.7.1

Format

A data frame contains 7 rows and 9 variables, with a column of "node" or first column of taxa labels.

Source

https://raw.githubusercontent.com/TreeViz/metastyle/master/design/viz_targets_exercise/tip_data.csv

Examples

data(df_tip_data)

Data set of the abundance and types of microbes

Description

The data set of abundance and types of microbes to be attached to the tree tips, provided by GraPhlAn (Asnicar et al. 2015).
Chap.10.3

Format

A data frame contains 332 rows and 4 variables,with a column of "node" or first column of taxa labels.

References

Asnicar, Francesco, George Weingart, Timothy L Tickle, Curtis Huttenhower, and Nicola Segata. Compact Graphical Representation of Phylogenetic Data and Metadata with GraPhlAn. PeerJ, 3: e1029, June 2015. doi:10.7717/peerj.1029

Examples

data(df_tippoint)

A DNAbin class to store the aligned sequnces of species of HPV58.tree

Description

A DNAbin class to store the aligned sequnces of species of HPV58.tree

Format

S3 class:DNAbin

References

Chen, Zigui, Wendy C. S. Ho, Siaw Shi Boon, Priscilla T. Y. Law, Martin C. W. Chan, Rob DeSalle, Robert D. Burk, and Paul K. S. Chan. Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants. Journal of Virology, Volume 91, Issue 21, November 2017, e01285–17. doi:10.1128/JVI.01285-17

Examples

data(dna_HPV58_aln)

Tree to display with symbolic points indicating partitioned bootstrap values

Description

This tree is to display with symbolic points with different color or shape indicating the bootstrap values belong to which category.
Catagories are defined by cutting the bootstrap values into several interval to indicate whether the clade is high, moderate or low support.
Chap.13.2

Format

character

Examples

data(text_RMI_tree)

Tree No.1 to display with visualized population genetics data

Description

Tree No.1 to display with visualized population genetics data for demonstrating the utility of ggtreeExtra.
Reproduction of Fig.4 of (Chow et al. 2020).
Chap.10.4

Format

S3 class:phylo

References

Chow, Nancy A., José F. Muñoz, Lalitha Gade, Elizabeth L. Berkow, Xiao Li, Rory M. Welsh, Kaitlin Forsberg, et al. Tracing the Evolutionary History and Global Expansion of Candida Auris Using Population Genomic Analyses. Edited by Geraldine Butler and Kirsten Nielsen. mBio, Volume 11, Issue 2, April 2020. doi:10.1128/mBio.03364-19

Examples

data(tree_Candidaauris)

Tree to display with dot and line plots of pairwise nucleotide sequence distances

Description

This tree is to provide accession numbers from its tip labels, which are used to calculates pairwise nucleotide sequence distances. The distance matrix then is visualized as dot and line plots and attached to the tree, demonstrating the abilities of facet_plot() of ggtree that can add multiple layers to a specific panel.
Reproduction fo Fig. 1 of (Chen et al. 2017).
Chap.13.1

Format

S3 class:phylo

References

Chen, Zigui, Wendy C. S. Ho, Siaw Shi Boon, Priscilla T. Y. Law, Martin C. W. Chan, Rob DeSalle, Robert D. Burk, and Paul K. S. Chan. Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants. Journal of Virology, Volume 91, Issue 21, November 2017, e01285–17. doi:10.1128/JVI.01285-17

Examples

data(tree_HPV58)

Tree No.2 to display with visualized population genetics data

Description

Tree No.2 to display with visualized population genetics data for demonstrating the utility of ggtreeExtra.
Reproduction of Fig 1 of (Wong et al. 2015).
Chap.10.4

Format

S3 class:phylo

References

Wong, Vanessa K., Stephen Baker, Derek J. Pickard, Julian Parkhill, Andrew J. Page, Nicholas A. Feasey, Robert A. Kingsley, et al. Phylogeographical Analysis of the Dominant Multidrug-Resistant H58 Clade of Salmonella Typhi Identifies Inter- and Intracontinental Transmission Events. Nature Genetics, Volume 47, Issue 6, May 2015, Pages 632–39. doi:10.1038/ng.3281

Examples

data(tree_NJIDqgsS)

Tree to color with continuous state transition in edges

Description

This tree is used to demonstrate the functionality of plotting continuous state transition in edges using the continuous parameter of ggtree.
Chap.4.3.5. This file is provided in http://www.phytools.org/eqg2015/asr.html.

Format

S3 class:phylo

Source

http://www.phytools.org/eqg2015/data/anole.tre

Examples

data(tree_anole)

Tree to be mapped to data

Description

This tree is used to demonstrate the functionality of the ⁠%<+%⁠ operator to attach annotation data to a ggtree graphic object.
Chap.7.1

Format

S3 class:phylo

Source

https://raw.githubusercontent.com/TreeViz/metastyle/master/design/viz_targets_exercise/tree_boots.nwk

Examples

data(tree_boots)

Tree to display with multiple graphs for multi-dimensional data

Description

This tree is to display with multiple graphs, and by reproducing Fig.2 of (Morgan, Segata, and Huttenhower 2013), demonstrates the feature of adding multiple layers to present different types of data by ggtreeExtra.
Chap.10.3

Format

S3 class:phylo

References

Morgan, Xochitl C., Nicola Segata, and Curtis Huttenhower. Biodiversity and Functional Genomics in the Human Microbiome. Trends in Genetics Volume 29, Issue 1, 2013 January, Pages 51–58. doi:10.1016/J.TIG.2012.09.005

Examples

data(tree_hmptree)

Tree to display with shrunk outlier long branch

Description

This tree is to display with display with shrunk outlier long branch to demonstrate how to shrink outlier long branch with ggtree by modifying coordination of the out groups, or with the ggbreak package.
Appendix.A.5.3

Format

S3 class:Phylo

Examples

data(tree_long_branch_example)

Tree to display with silhouettes from Phylopic

Description

This tree is to display with display with silhouettes from Phylopic, demonstrating the feature of ggtree that will automatically download phylopic figures by querying provided UID.
Chap.8.2

Format

S3 class:Phylo

Examples

data(tree_nex)

Tree to display with sampling information, SNP and Trait data

Description

The tree to display with sampling information, attached with dot chart of SNP and bar chart of Trait data.
Chap.7.2

Format

S3 class:phylo

Source

https://raw.githubusercontent.com/katholt/plotTree/master/tree_example_april2015/tree.nwk

Examples

data(tree_nwk)

Tree to display with multiple sequence alignment

Description

This tree is used to display with multiple sequence alignment.
Chap.7.4

Format

S3 class:phylo

Examples

data(tree_seq_nwk)

Tree to group and highlight

Description

This tree is used to reproduce Figure 1 of (Larsen et al. 2019) with grouping, highlighting and labelling.
Chap.13.3

Format

S3 class:Phylo

References

Larsen, Frederik T., Bertrand Bed’Hom, Bernt Guldbrandtsen, and Tina S. Dalgaard. Identification and Tissue-Expression Profiling of Novel Chicken c-Type Lectin-Like Domain Containing Proteins as Potential Targets for Carbohydrate-Based Vaccine Strategies. Molecular Immunology, Volume 114, Issue October, October 2019, pages 216–25. doi:10.1016/j.molimm.2019.07.022

Examples

data(tree_treenwk_30.4.19)