gtollefson/Northern_Ethiopia_Pf_ARTR_2025_Project
Domaine:
healthcareType de record:
software
Créateur:
gto
Hôte:
Scripts and input data to prepare main figures for our paper titled: Rising widespread Kelch13 R622I and detection of C580Y of African origin in Plasmodium falciparum in northern Ethiopia further threaten artemisinin-based therapies
This repository contains all data and code used to generate the analyses and figures presented in the manuscript:
*“Rising widespread Kelch13 R622I and detection of C580Y of African origin in *Plasmodium falciparum* in northern Ethiopia further threaten artemisinin-based therapies”*
GT will add preprint author list here when uploaded and ultimately the citation to peer reviewed paper
## Repository Structure
```bash
.
├── Fig1/ # Scripts and outputs for Figure 1 (Prevalence and geography)
├── Fig2/ # Scripts and outputs for Figure 2 (Haplotype comparison)
├── Fig3/ # Scripts and outputs for Figure 3 (Drug resistance combinations)
├── Fig4/ # Scripts and outputs for Figure 4 (IBD and clonal network analyses)
├── Fig5/ # Scripts and outputs for Figure 5 (Temporal trends and relatedness)
├── data/ # Input data (genotype data, metadata, COI, IBD, rainfall, case counts, mapping geojson)
└── README.md # Project overview and usage instructions
```
## Getting Started
1. Clone the repository
```bash
git clone github.com
cd Northern_Ethiopia_Pf_ARTR_2025_Project
```
2. Install dependencies
R (Figures 1, 3, 4, 5)
Ensure the following R packages are installed:
```r
install.packages(c(
"dplyr", "ggplot2", "ggpubr", "ggsignif", "igraph", "ggraph",
"tidygraph", "rstatix", "sf", "readr", "stringr", "tidyr", "viridis", "terra"
))
```
Python (Figure 2)
Python dependencies (e.g. pandas, matplotlib, scikit-learn) can be installed via:
```bash
pip install numpy==1.24.4 pandas==1.5.3 matplotlib==3.7.1 seaborn==0.12.2 scipy==1.10.1 tqdm==4.65.0
```
## Figures Overview
**Figure 1:**
Geographic and statistical summary of K13 622I mutation prevalence and pfhrp2-based RDT negativity across districts, kebeles, and RDT result categories in Northwest Ethiopia.
**Figure 2:**
Flanking haplotype comparison shows simil …