This repository contains scripts to reproduce analysis and figures presented in the manuscript Maver et al. 2021, describing the effects of an external addition of the alkaloid gramine on the rhizosphere microbiota recruitment in modern barley plants.
List of files:
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gramine_microbiome.Rproj- Rproject file of this repository -
dada2_asv_scripts- folder containing files, scripts and html export of notebook to reproduce the ASVs picking strategy described in the manuscript -
sessioninfo.text- packages used for calculations -
Map_JH12_2.txt- Mapping file of the experiment -
JH12_object_construction_v0621_ASVs.RandJH12_object_construction_v0221_genus.R- scripts for quality filtering and phyloseq object construction
Main figures:
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JH12_Figure_1_alpha.R- script for Figure 1 alpha-diversity calculations -
JH12_Figure_2_beta.R- script for Figure 2 beta-diversity calculations + Supp. Figure S3 beta-diversity -
JH12_Figure_3_4.R- script for Figures 3 DeSeq, UpSetR plot and Figure 4 Heatmap -
JH12_Figure_5.R- script for Figure 5 Ternary plots
Supplementary figures:
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JH12_Figure_S1.R- script for Supp. Figure S1 Adsorption models -
JH12_Figure_S2.R- script for Supp. Figure S2 Dry Weight -
JH12_Figure_S4.R- script for Supp. Figure S4 alpha-diversity ASVs calculations -
JH12_Figure_S5.R- script for Supp. Figure S5 beta-diversity calculations ASVs calculations