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README.rmd
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---
output:
md_document:
variant: gfm
html_preview: false
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
# Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree
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
## 1. `exampledata`
This directory contains example input data files for phylogenetic analysis and tree placements.
### `Holomycota`:
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.
### `Mitsi`:
Contains files from the Mitsi dataset.
- **`rsbl20190182supp2.jplace`**: Placement file for the Mitsi dataset.
- **`rsbl20190182supp7.tre`**: Tree file corresponding to the placement data.
### `subtree`:
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.
---
## 2. `pdf`
This directory contains PDF files of the figures generated from the analysis.
- **`Fig1.pdf`**Workflow diagram of treeio and ggtree in processing phylogenetic placement data, **`Fig2.pdf`**, **`Fig3.pdf`**,**`Fig4.pdf`**: Figures representing various visualizations of the phylogenetic analysis. **`FigS1.pdf`**:Supplementary figure showing detailed performance evaluations of treeio, including runtime and memory efficiency when processing large phylogenetic trees with diverse placement scenarios.
---
## 3. `Rmarkdown`
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.
---
## 4. `tiff`
This directory contains TIFF versions of the figures for high-quality image export.
- **`Fig2.tiff`**, **`Fig3.tiff`**, **`Fig4.tiff`**: High-resolution images of the figures in TIFF format.
---
## 5. `simulated_data`
This directory contains files and scripts for simulated data analysis.
- **`scripts`**
Contains R scripts for generating and visualizing simulated data:
- **`plot_simulated_jplace.R.r`**: Script for visualizing simulated `.jplace` files.
- **`run_simulate_jplace.R`**: Script for generating simulated `.jplace` data.
- **`simulated_jplace`**
Contains simulated `.jplace` files with different configurations:
- **`simulate_tips100000_placement_nrow_1000000.jplace`**
- **`simulate_tips100000_placement_nrow_100000.jplace`**
- **`simulate_tips100000_placement_nrow_10000.jplace`**
- **`simulate_tips100000_placement_nrow_1000.jplace`**
- (and others with similar naming patterns).
- **`src`**
Contains alternative versions of scripts for generating and visualizing simulated data:
- **`plot_simulated_jplace.R.r`**
- **`run_simulate_jplace.R`**
- **Other Files**
Test `.jplace` files with different sample sizes and row configurations for validation:
- **`test_jp_1k_1kp.jplace`**, **`test_jp_1k_10kp.jplace`**, **`test_jp_1k_100kp.jplace`**, **`test_jp_1k_1000kp.jplace`**
- **`test_jp_10k_1kp.jplace`**, **`test_jp_10k_10kp.jplace`**, **`test_jp_10k_100kp.jplace`**, **`test_jp_10k_1000kp.jplace`**
- **`test_jp_50k_1kp.jplace`**, **`test_jp_50k_10kp.jplace`**, **`test_jp_50k_50kp.jplace`**, **`test_jp_50k_100kp.jplace`**
- **`test_jp_100k_1kp.jplace`**, **`test_jp_100k_10kp.jplace`**, **`test_jp_100k_50kp.jplace`**, **`test_jp_100k_100kp.jplace`**
- (and others with similar naming patterns).
---
## Usage
- 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.
---
## Requirements
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.