Scripts in order of processing for bacteria and fungal datasets:
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bioinformatics_16S.R -- processing of raw 16S rRNA sequences. Mostly follows tutorial found at https://github.com/fiererlab/dada2_fiererlab and on B. Callahan (author of dada2) website.
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bioinformatics_final_ITS.R -- processing of raw ITS region sequences. Nearly identical pipeline to 16S above, but with some steps modified to reflect ITS primers and sequences
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full16S_EDA_part1_Sept.R -- bacteria/archaea (16S) data cleaning, archaea and contaminant checking/removal, rarefying
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fullITS_EDA_part1_Sept.R -- fungi (ITS) data cleaning and contaminant checking/removal, rarefying
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full16S_EDArarefied_part2_Sept.R -- bacteria (16S) exploratory data analysis and sample type analysis and plots
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fullITS_EDArarefied_Part2_Sept.R -- fungi (ITS) exploratory data analysis and sample type analysis and plots
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habitatAnalyses_Sept.R -- bacterial and fungal analyses exploring differences in open patch and forested matrix, including compositional and biomass potential differences
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I6S_sourceTracking_Sept.R -- analyses to determine origin of bacteria in bioaerosols
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ITS_sourceTracking_Sept.R -- analyses to determine origin of bacteria in fungi
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ANCOMBC_robust_foliarAir_pt0.05.R -- performs ANCOMBC-2 analyses to determine differentially abundant taxa between bioaerosols and foliar surfaces for both bacterial and fungal datasets.
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bacteriaSporesAndPigment.R -- infers pigmentation and sporulation status for ANCOM-identified ASVs using Madin et al. 2020 and ijsem databases
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ANCOM_traits_I6SandITS_.05pct.R -- stats for how foliar surface and biaoerosol enriched taxa differ in traits. Both bacterial traits, just morphology (inference from FUNGuild and stats) for fungi.
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sporeSize.05pct.R -- infers spore size for fungi (using Aguilar- Trigueros et al. 2023 dataset) and associated stats.
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weather_qPCRtable -- creates formatted meteorological and qPCR plots for supplement.
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figureBeautifying.R --beautifies paper figures together
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NCBIuploads.R -- formatting metadata for Bioproject and SRA