This repository contains the dataflow and scripts used to process the COI and 18S metabarcode reads in the paper Robinson et al., 2022 (Scientific Reports, Accepted).
Robinson, C. V., Porter, T. M., McGee, K. M., McCusker, M., Wright, M. T. G., & Hajibabaei, M. (2022). Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour. BioRxiv, 35. doi: https://doi.org/10.1101/2022.04.17.488590
Infiles, R scripts, and supplementary data files can be downloaded from https://github.com/Hajibabaei-Lab/RobinsonEtAl2022_TorontoHarbour/releases .
SitesCSOs.csv
metadata.csv
TH_extra_data.txt
diversity.metrics.csv
results_F230R_10Aug20.csv
results_ml-jg_10Aug20.csv
morph_new.csv
results_18S_v4.1.csv
EPA_families.csv
Freshwaterecol_Moog.csv
Freshwater_Tachet.csv
To try to improve reproducibility, script libraries are loaded using groundhog but libraries but if you prefer libraries can be loaded the usual way with minor changes. Running these scripts in order ensures that the necessary directories are set up for subsequent scripts.
Fig1_mapped_gradients.R uses SitesCSOs.csv, metadata.csv, TH_extra_data.txt, and diversity.metrics.csv (from Fig5_hierarchical_partitioning.R) to produce Fig1_mapped_gradients.pdf .
Fig2_richness.R uses results_F230R_10Aug20.csv, results_ml-jg_10Aug20.csv, morph_new.csv, and results_18S_v4.1.csv to produce Fig2_richness.pdf .
Fig3_PCA_NMDS.R uses results_F230R_10Aug20.csv, results_ml-jg_10Aug20.csv, momrph_new.csv, SitesCSOs.csv, metadata.csv, TH_extra_data.txt, and results_18S_v4.1.csv to produce Fig3_PCA_NMDS.pdf as well as a suite of supporting files.
Fig4_relative_abundance.R uses results_F230R_10Aug20.csv, results_ml-jg_10Aug20.csv, morph_new.csv, results_18S_v4.1.csv, EPA_families.csv, Freshwaterecol_Moog.csv, and Freshwater_Tachet.csv to produce Fig4_relative_abundance.pdf.
Fig5_hierarchical_partitioning.R uses results_F230R_10Aug20.csv, results_ml-jg_10Aug20.csv, morph_new.csv, results_18S_v4.1.csv, metadata.csv, and TH_extra_data.txt to produce Fig5_hierarchical_partitioning.pdf, the results summarized in Table S5 and Table S6, and a couple other supporting files.
FigS1_resolution_rarefaction.R uses results_F230R_10Aug20.csv, results_ml-jg_10Aug20.csv, results_18S_v4.1.csv, and morph_new.csv to produce FigS1_resolution_rarefaction.pdf.
FigS2_predictor_correlations.R uses metadata.csv and TH_extra_data.txt to produce FigS2_predictor_correlations.pdf.
TableS3_checklist.R uses morph_new.csv, results_F230R_10Aug20.csv, results_ml-jg_10Aug20.csv, and results_18S_v4.1.csv to produce checklists that were compiled into Table S3 (excel spreadsheet).
Robinson, C.V., Porter, T.M., McGee, K.M., McCusker, M., Wright, M.T.G., Hajibabaei, M. 2022. Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour. Scientific Reports, Accepted.
Last updated: May 27, 2022