If you use this work in published research, please cite:

Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree

This repo contains source code and data to produce Supplementary Material of the above paper.

https://github.com/YuLab-SMU/Supplemental_ggtree_placement

This directory contains example input data files for phylogenetic analysis and tree placements.

Contains jplace and CSV files related to the Holomycota dataset.

• HolomycotaV4_alignedtrim.jplace: Placement file for the Holomycota phylogenetic analysis.
• V4_group.csv: Associated metadata for the groups in the Holomycota dataset.

Contains files from the Mitsi dataset.

• rsbl20190182supp2.jplace: Placement file for the Mitsi dataset.
• rsbl20190182supp7.tre: Tree file corresponding to the placement data.

Contains data for a specific subtree analysis.

• Amt_tiplabel.csv: Tip label information for the Amt subtree.
• pplacer_Amt_subtree.jplace: Placement file for the Amt subtree analysis.

This directory contains PDF files of the figures generated from the analysis.

• Fig1.pdf, Fig2.pdf, Fig3.pdf: Figures representing various visualizations of the phylogenetic analysis.

This directory contains an R Markdown file used for generating the supplementary files for the project.

• header.tex: LaTeX header for formatting the supplementary file.
• supplementary_filev2.Rmd: R Markdown source file for generating the supplementary file.
• supplementary_filev2.pdf: PDF version of the supplementary file.

This directory contains TIFF versions of the figures for high-quality image export.

• Fig1.tiff, Fig2.tiff, Fig3.tiff: High-resolution images of the figures in TIFF format.

• The exampledata directory contains the input data files used in the analysis.
• Figures are stored in both PDF and TIFF formats for use in publications or presentations.
• The Rmarkdown directory contains the source file for generating the supplementary materials, which can be edited or recompiled if needed.

To reproduce the figures and analyses, you will need:

• R with necessary packages such as ggtree, treeio, dplyr, and ggplot2.
• LaTeX for compiling the R Markdown file to PDF.