This repository contains the code needed to reproduce figures for for Gupta & Poret et al.'s "Cutaneous surgical wounds have distinct microbiomes from intact skin" (10.1128/spectrum.03300-22, raw data can be found at: PRJNA809947). A description of each file uploaded will be included below.
SG_AJP_wound_microbiome_figure_creation.m is the MATLAB script used to generate all figures used in this paper. Associated function files needed to run this script are stored in \matlab_functions. This script intakes batch_1_2_QIIME2_output.xlsx, batch_3_QIIME2_output.xlsx, clinical_metadata.xlsx, distance-matrix_final.xlsx, and patient_sequencing_metadata.xlsx and outputs both images and files that will be saved in a subdirectory /saved_excel_files. The excel files are saved in the format {date}_OTUs_combined_batches.xlsx, {date}_all_unique_taxons.xlsx, {date}_species_counts.xlsx, {date}_unique_genus_counts.xlsx, and contain raw OTU counts, counts combined by taxon (ex. all Cutibacterium acnes labeled taxons are combined in this sheet), counts grouped by genus, and counts grouped by species. All these excel sheets contain data post-quality-control filtering, and the {date} refers to the date of file generation.
Raw data from QIIME2 is outputted in batch_1_2_QIIME2_output.xlsx and batch_3_QIIME2_output.xlsx. Clinical metadata (i.e. tumor type, age, sex, etc.) is stored in clinical_metadata.xlsx and sequencing metadata is stored in patient_sequencing_metadata.xlsx. A unifrac distance matrix generated from filtered all OTUs present in {date}_OTUs_combined_batches is written to distance-matrix_final.xlsx.