├── HPV58.tree ├── HPV58_aln.fas ├── README.md ├── header.tex ├── plotTree ├── README.md ├── plotTree.R ├── plotTree.py ├── plotTreeShiny │ ├── plotTree.R │ ├── server.R │ └── ui.R ├── server_modified │ ├── server.R │ └── ui.R ├── shiny_practice │ ├── print_statemtn.r │ ├── reactive │ │ ├── plot.pdf │ │ ├── plotTree.R │ │ ├── server.R │ │ └── ui.R │ ├── reactive_stable │ │ ├── plotTree.R │ │ ├── server.R │ │ └── ui.R │ ├── runPlotTree.download │ │ ├── plotTree.R │ │ ├── server.R │ │ └── ui.R │ ├── runPlotTree │ │ ├── plotTree.R │ │ ├── server.R │ │ └── ui.R │ ├── runPlotTree_conditional │ │ ├── plotTree.R │ │ ├── server.R │ │ └── ui.R │ ├── runPlotTree_conditional_clustering │ │ ├── plotTree.R │ │ ├── server.R │ │ └── ui.R │ ├── runPlotTree_tabs │ │ ├── plotTree.R │ │ ├── server.R │ │ └── ui.R │ ├── uploadTree2 │ │ ├── server.R │ │ └── ui.R │ ├── variable_relationships.txt │ └── wan │ │ ├── server.R │ │ └── ui.R └── tree_example_april2015 │ ├── .Rhistory │ ├── alleles.csv │ ├── bar.csv │ ├── blocks.csv │ ├── blocks.txt │ ├── info.csv │ ├── info.pdf │ ├── info.png │ ├── myplot.pdf │ ├── myplot4.pdf │ ├── pan.csv │ ├── pan.pdf │ ├── pan.png │ ├── res_genes.csv │ ├── res_genes.pdf │ ├── res_genes.png │ ├── tree.nwk │ └── tree_examples.txt ├── supp.bib ├── supplemental_file.Rmd └── supplemental_file.pdf /HPV58.tree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GuangchuangYu/plotting_tree_with_data/HEAD/HPV58.tree -------------------------------------------------------------------------------- /HPV58_aln.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GuangchuangYu/plotting_tree_with_data/HEAD/HPV58_aln.fas -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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