Objective

• Fields of Study:

  • Data Science

  • R Shiny

  • Biology (Taxonomy and Phylogeny)

• Goal:

  • Visualize related plant groups along a phylogenetic tree for the angiosperm phylum.

Background

• Taxonomy and Phylogenetic Tree:

  • Phylum

  • Class

  • Order

  • Family

  • Genus

  • Species

Additional Criteria

• Adaptability:

  • Plant phylogenies are ever-changing.

  • The tool will be taught beyond Spring 2024.

• Usability:

  • Intuitive for students to use.

• Compatibility:

  • Data processing compatible with updated data sets.

• User-Friendly:

  • Coding is not a learning outcome of The Evolution of Plant Diversity.

  • Back-end code annotated, flexible, and easy-to-read.

Milestones

1. Background:

   • Understand tree data formats.

   • Review course material.

   • Generate simple trees in R.

2. Find Data Set:

   • Acquire data set covering the most recent phylogeny from angiosperm phylum to family.

3. Function Search:

   • Implement functions for visualization, pruning, and classification.

   • Color coding classifications and annotating tips and nodes.

4. Presentation:

   • Format into interactive R Shiny webpage.

R Packages

• ggtree: Reads Newick tree files, plots phylogenetic trees.

  • Functions:

    • read.tree: Reads tree files.

    • AllTipLabels: Labels all tips of a phylogenetic tree.

    • keep.tip: Keeps only the user-selected tips.

    • $node.label: Labels selected nodes.

    • extract.clade: Extracts user-selected clades.

• TreeTools: Additional functions for tree manipulation.

• ape: Functions for analyzing phylogenetic and evolutionary relationships.

Product

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Reflection

• Time-Management: Met weekly research and technical demands.

• Creative-Thinking: Brainstorming and decision-making.

• Problem-Solving: Troubleshooting and external research.

• Technical Skills: Data manipulation, R Shiny.

• Interpersonal Skills: Collaboration and teamwork.