,
Shuangbin Xu [aut] ,
Lin Li [aut] | Title: | Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242) |
|---|---|
| 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, doi:10.1201/9781003279242). |
| Authors: | Guangchuang Yu [aut, cre, cph]
,
Shuangbin Xu [aut] ,
Lin Li [aut] |
| Maintainer: | Guangchuang Yu <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 0.0.6 |
| Built: | 2024-11-11 04:44:01 UTC |
| Source: | https://github.com/yulab-smu/tdbook |
This data set contains multiple sequence alignment information to be
attached to the tree.
Chap.7.4
AAbin
data(AA_sequence)data(AA_sequence)
The allele table with original data to be processed to SNP data. Then attached
to the tree after visualizing.
Chap.7.2
A data frame contains 386 rows and 385 variables, with first row of tips labels.
https://raw.githubusercontent.com/katholt/plotTree/master/tree_example_april2015/alleles.csv
data(df_alleles)data(df_alleles)
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
A data frame to store taxonomy information, contains 1351 rows and 7 variables (classification levels).
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
data(df_alltax_info)data(df_alltax_info)
The trait data to be visualized with bar plot and attached to the tree.
Chap.7.2
A data frame contains 386 rows and 2 variables, with a column of "node" or first column of taxa labels.
https://raw.githubusercontent.com/katholt/plotTree/master/tree_example_april2015/bar.csv
data(df_bar_data)data(df_bar_data)
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
A data frame contains 332 rows and 3 variables, with a column of "node" or first column of taxa labels.
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
data(df_barplot_attr)data(df_barplot_attr)
Population genetics data to be visualized using multiple graphs and
attached to tree No.1 with geo_fruit() of ggtreeExtra.
Chap.10.4
A data frame contains 305 rows and 20 variables, with a column of "node" or first column of taxa labels.
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
data(df_Candidaauris_data)data(df_Candidaauris_data)
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
A data frame contains 36 rows and 3 variables.
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
data(df_difftax)data(df_difftax)
The sampling information data set be attached to the tree tip.
Chap.7.2
A data frame contains 386 rows and 6 variables, with a column of "node" or first column of taxa labels.
https://raw.githubusercontent.com/katholt/plotTree/master/tree_example_april2015/info.csv
data(df_info)data(df_info)
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
A data frame with 6 rows and 6 variables with a column of node or first column of taxa labels.
data(df_inode_data)data(df_inode_data)
Population genetics data to be visualized using multiple graphs and
attached to tree No.2 with geo_fruit() of ggtreeExtra.
Chap.10.4
A data frame contains 1351 rows and 7 variables, with a column of "node" or first column of taxa labels.
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
data(df_NJIDqgsS)data(df_NJIDqgsS)
The data set of abundance of microbes at different body sites to be
visualized using heatmap and attached to the tree.
Chap.10.3
A data frame contains 2324 rows and 3 variables, with a column of "node" or first column of taxa labels.
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
data(df_ring_heatmap)data(df_ring_heatmap)
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.
A data frame contains 100 rows and 1 variables.
http://www.phytools.org/eqg2015/data/svl.csv
data(df_svl)data(df_svl)
This data contains annotation information about tips of tree_boots,
that is to be mapped to the tree using the %<+% operator.
Chap.7.1
A data frame contains 7 rows and 9 variables, with a column of "node" or first column of taxa labels.
https://raw.githubusercontent.com/TreeViz/metastyle/master/design/viz_targets_exercise/tip_data.csv
data(df_tip_data)data(df_tip_data)
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
A data frame contains 332 rows and 4 variables,with a column of "node" or first column of taxa labels.
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
data(df_tippoint)data(df_tippoint)
A DNAbin class to store the aligned sequnces of species of HPV58.tree
S3 class:DNAbin
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
data(dna_HPV58_aln)data(dna_HPV58_aln)
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
character
data(text_RMI_tree)data(text_RMI_tree)
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.
S3 class:phylo
http://www.phytools.org/eqg2015/data/anole.tre
data(tree_anole)data(tree_anole)
This tree is used to demonstrate the functionality of the %<+% operator
to attach annotation data to a ggtree graphic object.
Chap.7.1
S3 class:phylo
data(tree_boots)data(tree_boots)
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
S3 class:phylo
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
data(tree_Candidaauris)data(tree_Candidaauris)
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
S3 class:phylo
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
data(tree_hmptree)data(tree_hmptree)
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
S3 class:phylo
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
data(tree_HPV58)data(tree_HPV58)
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
S3 class:Phylo
data(tree_long_branch_example)data(tree_long_branch_example)
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
S3 class:Phylo
data(tree_nex)data(tree_nex)
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
S3 class:phylo
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
data(tree_NJIDqgsS)data(tree_NJIDqgsS)
The tree to display with sampling information, attached with dot chart of SNP
and bar chart of Trait data.
Chap.7.2
S3 class:phylo
https://raw.githubusercontent.com/katholt/plotTree/master/tree_example_april2015/tree.nwk
data(tree_nwk)data(tree_nwk)
This tree is used to display with multiple sequence alignment.
Chap.7.4
S3 class:phylo
data(tree_seq_nwk)data(tree_seq_nwk)
This tree is used to reproduce Figure 1 of (Larsen et al. 2019) with
grouping, highlighting and labelling.
Chap.13.3
S3 class:Phylo
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
data(tree_treenwk_30.4.19)data(tree_treenwk_30.4.19)