This dataset contains R-scripts to perform bioinformatic and statistical analysis on leaf-associated fungal communities of wild plant populations (Ma et al. Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Submitted). Raw sequences are available at https://doi.org/10.15454/X23KJF. Metadata and ASV tables are also provided allowing to use statistical analysis scripts without running the bioinformatic steps.