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

## Documentation for package ‘TDbook’ version 0.0.5

- DESCRIPTION file.

## Help Pages

AA_sequence | Data set containing multiple sequence alignment information
data-AA_sequence | Data set containing multiple sequence alignment information
data-df_alleles.csv | Allele table
data-df_alltax_info | Data frame containing hierarchical relationship
data-df_barplot_attr | Data set of the abundance of microbes at the body sites of greatest prevalence
data-df_bar_data | Trait data
data-df_Candidaauris_data | Population genetics data No.1
data-df_difftax | Data frame containing taxa and factor information and pvalue
data-df_info | Sampling information data set
data-df_inode_data | Nodedata to be mapped to tree
data-df_NJIDqgsS | Population genetics data No.2
data-df_ring_heatmap | Data set of the abundance and types of microbes
data-df_svl | Data frame containing slv information
data-df_tippoint | Data set of the abundance and types of microbes
data-df_tip_data | Tipdata to be mapped to tree
data-dna_HPV58_aln | A DNAbin class to store the aligned sequnces of species of HPV58.tree
data-text_RMI_tree | Tree to display with symbolic points indicating partitioned bootstrap values
data-tree_anole | Tree to color with continuous state transition in edges
data-tree_boots | Tree to be mapped to data
data-tree_Candidaauris | Tree No.1 to display with visualized population genetics data
data-tree_hmptree | Tree to display with multiple graphs for multi-dimensional data
data-tree_HPV58 | Tree to display with dot and line plots of pairwise nucleotide sequence distances
data-tree_long_branch_example | Tree to display with shrunk outlier long branch
data-tree_nex | Tree to display with silhouettes from Phylopic
data-tree_NJIDqgsS | Tree No.2 to display with visualized population genetics data
data-tree_nwk | Tree to display with sampling information, SNP and Trait data
data-tree_seq_nwk | Tree to display with multiple sequence alignment
data-tree_treenwk_30.4.19 | Tree to group and highlight
df_alleles | Allele table
df_alltax_info | Data frame containing hierarchical relationship
df_barplot_attr | Data set of the abundance of microbes at the body sites of greatest prevalence
df_bar_data | Trait data
df_Candidaauris_data | Population genetics data No.1
df_difftax | Data frame containing taxa and factor information and pvalue
df_info | Sampling information data set
df_inode_data | Nodedata to be mapped to tree
df_NJIDqgsS | Population genetics data No.2
df_ring_heatmap | Data set of the abundance and types of microbes
df_svl | Data frame containing slv information
df_tippoint | Data set of the abundance and types of microbes
df_tip_data | Tipdata to be mapped to tree
dna_HPV58_aln | A DNAbin class to store the aligned sequnces of species of HPV58.tree
text_RMI_tree | Tree to display with symbolic points indicating partitioned bootstrap values
tree_anole | Tree to color with continuous state transition in edges
tree_boots | Tree to be mapped to data
tree_Candidaauris | Tree No.1 to display with visualized population genetics data
tree_hmptree | Tree to display with multiple graphs for multi-dimensional data
tree_HPV58 | Tree to display with dot and line plots of pairwise nucleotide sequence distances
tree_long_branch_example | Tree to display with shrunk outlier long branch
tree_nex | Tree to display with silhouettes from Phylopic
tree_NJIDqgsS | Tree No.2 to display with visualized population genetics data
tree_nwk | Tree to display with sampling information, SNP and Trait data
tree_seq_nwk | Tree to display with multiple sequence alignment
tree_treenwk_30.4.19 | Tree to group and highlight