jaumlrc/Immstat_cure

Contains the scripts and test files for the manuscript "Systemic inflammatory markers of VL treatment response in East Africa" # Immstat_cure ## Overview This repository contains the R script used for data analysis in the manuscript **“Systemic inflammatory markers of VL treatment response in East Africa.”** --- ## Required Libraries The script depends on the following R packages: `ggplot2`, `reshape2`, `viridis`, `dplyr`, `tidyr`, `ggpubr`, `rstatix`, `factoextra`, `ggrepel`, `plotly`, `umap`, `pheatmap`, `Hmisc`, `corrplot`, `ggradar`, `fmsb`, `scales`, `cowplot`, `ggiraphExtra`, `grid`, `gridExtra`, `ggprism`, `ggfortify`, `cluster`, `caret`, `mixOmics`, `sva`, `logistf`, `ggpointdensity`, `MASS`, `ggVennDiagram`, `tibble`, `ggtext`. --- ## Used Library versions: `ggplot2(v 3.5.1)`, `reshape2(v 1.4.4)`, `viridis(v 0.6.5)`, `dplyr(v 1.1.4)`, `tidyr(v 1.3.1)`, `ggpubr(v 0.6.0)`, `rstatix(v 0.7.2)`, `factoextra(v 1.0.7)`, `ggrepel(v 0.9.6)`, `plotly(v 4.10.4)`, `umap(v 0.2.10.0)`, `pheatmap(v 1.0.12)`, `Hmisc(v 5.2.2)`, `corrplot(v 0.95)`, `ggradar(v 0.2)`, `fmsb(v 0.7.6)`, `scales(v 1.3.0)`, `cowplot(v 1.1.3)`, `ggiraphExtra(v 0.3.0)`, `grid(v 4.4.2)`, `gridExtra(v 2.3)`, `ggprism(v 1.0.5)`, `ggfortify(v 0.4.17)`, `cluster(v 2.1.8)`, `caret(v 7.0.1)`, `mixOmics(v 6.30.0)`, `sva(v 3.54.0)`, `logistf(v 1.26.1)`, `ggpointdensity(v 0.1.0)`, `MASS(v 7.3.65)`, `ggVennDiagram(v 1.5.2)`, `tibble(v 3.2.1)`, `ggtext(v 0.1.2)`. --- ## Script Functions - Polishes the data and generates quality control plots - Separates the data by male and female patients - Generates and plots PCA and UMAP visualizations - Compares pre- and post-treatment data - Identifies potential markers linked to clinical states --- ## Input Files The script **`Legendplex_clinical_data_analysis.v7.R`** expects **three input files** (one set per country): 1. **Patient clinical metadata** 2. **Patient Legendplex results** 3. **Legendplex Limits of Quantification (LOQ)** --- ## Example Input Data *(Note: These examples do not represent real data)* ### 1. Legendplex Results ``` $ well experiment sample dilution replica …