BranchesTags

Repository files navigation

BioNI Analysis Scripts

This repository contains the R scripts used for data analysis and figure generation in the manuscript.

The analyses are organised into three main project folders according to the corresponding figures:

  • 01_BNI_approaches_and_plant_traits contains the analyses and plotting scripts for Figures 1 and 2.
  • 02_root_exudate_metabolomics contains the analyses and plotting scripts for Figure 3.
  • 03_sequencing_analysis contains the analyses and plotting scripts for Figure 4.

Project structure

Each project follows a consistent directory structure:

00_input/
01_rmd/
02_docs/
03_analysis/
R/
.here
*.Rproj

00_input

Contains the input data required for the analyses, including processed experimental data, metadata, and other analysis-ready datasets.

01_rmd

Contains the main R Markdown (.Rmd) files used to run the analyses, together with the corresponding rendered HTML files for convenient viewing of the analysis workflow and outputs.

02_docs

Contains supporting documents where necessary.

03_analysis

Contains intermediate and final outputs generated by the workflows in 01_rmd, including processed datasets, statistical results, tables, and figures.

R

Contains project-level R scripts used to support the analysis workflow, including configuration, project initialisation, and reusable helper functions.

  • config.R defines project-wide settings, parameters, and other configuration options used across analyses.
  • init_project.R initialises the analysis environment and loads the required project settings and supporting scripts.
  • utils.R contains reusable utility functions shared across multiple R Markdown files.

Separating these supporting scripts from the main analysis files helps maintain a consistent and reproducible workflow across analyses.

.here

The .here file defines the project root for the here R package. This allows file paths to be specified relative to the project root rather than using machine-specific absolute paths, improving portability and reproducibility.

.Rproj

The .Rproj file defines the corresponding RStudio project. Opening this file provides a consistent project environment and ensures that the analyses are run from the appropriate project directory.

Note on table numbering and order

The numbering and order of tables generated within the analysis scripts do not necessarily correspond to those of the supplementary tables submitted with the manuscript.

In the code repository, tables are organised according to the analytical workflow and their direct relationship to individual analyses. In the submitted Supplementary Information, tables are renumbered and ordered according to their sequence in the manuscript.

About

R scripts used for data processing, statistical analysis and visualisation in the BioNI wheat study.

Topics

bnimetabolomicsnitrificationsoil-microbiologywheat

Resources

Readme
Activity

Stars

0 stars

Watchers

0 watching

Forks

0 forks
Report repository

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
BioNI Analysis Scripts
This repository contains the R scripts used for data analysis and figure generation in the manuscript.
The analyses are organised into three main project folders according to the corresponding figures:
  • 01_BNI_approaches_and_plant_traits contains the analyses and plotting scripts for Figures 1 and 2.
  • 02_root_exudate_metabolomics contains the analyses and plotting scripts for Figure 3.
  • 03_sequencing_analysis contains the analyses and plotting scripts for Figure 4.
Project structure
Each project follows a consistent directory structure:
00_input/
01_rmd/
02_docs/
03_analysis/
R/
.here
*.Rproj

00_input
Contains the input data required for the analyses, including processed experimental data, metadata, and other analysis-ready datasets.
01_rmd
Contains the main R Markdown (.Rmd) files used to run the analyses, together with the corresponding rendered HTML files for convenient viewing of the analysis workflow and outputs.
02_docs
Contains supporting documents where necessary.
03_analysis
Contains intermediate and final outputs generated by the workflows in 01_rmd, including processed datasets, statistical results, tables, and figures.
R
Contains project-level R scripts used to support the analysis workflow, including configuration, project initialisation, and reusable helper functions.
  • config.R defines project-wide settings, parameters, and other configuration options used across analyses.
  • init_project.R initialises the analysis environment and loads the required project settings and supporting scripts.
  • utils.R contains reusable utility functions shared across multiple R Markdown files.
Separating these supporting scripts from the main analysis files helps maintain a consistent and reproducible workflow across analyses.
.here
The .here file defines the project root for the here R package. This allows file paths to be specified relative to the project root rather than using machine-specific absolute paths, improving portability and reproducibility.
.Rproj
The .Rproj file defines the corresponding RStudio project. Opening this file provides a consistent project environment and ensures that the analyses are run from the appropriate project directory.
Note on table numbering and order
The numbering and order of tables generated within the analysis scripts do not necessarily correspond to those of the supplementary tables submitted with the manuscript.
In the code repository, tables are organised according to the analytical workflow and their direct relationship to individual analyses. In the submitted Supplementary Information, tables are renumbered and ordered according to their sequence in the manuscript.
About
R scripts used for data processing, statistical analysis and visualisation in the BioNI wheat study.
Topics
bnimetabolomicsnitrificationsoil-microbiologywheat
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
BioNI Analysis Scripts
This repository contains the R scripts used for data analysis and figure generation in the manuscript.
The analyses are organised into three main project folders according to the corresponding figures:
  • 01_BNI_approaches_and_plant_traits contains the analyses and plotting scripts for Figures 1 and 2.
  • 02_root_exudate_metabolomics contains the analyses and plotting scripts for Figure 3.
  • 03_sequencing_analysis contains the analyses and plotting scripts for Figure 4.
Project structure
Each project follows a consistent directory structure:
00_input/
01_rmd/
02_docs/
03_analysis/
R/
.here
*.Rproj

00_input
Contains the input data required for the analyses, including processed experimental data, metadata, and other analysis-ready datasets.
01_rmd
Contains the main R Markdown (.Rmd) files used to run the analyses, together with the corresponding rendered HTML files for convenient viewing of the analysis workflow and outputs.
02_docs
Contains supporting documents where necessary.
03_analysis
Contains intermediate and final outputs generated by the workflows in 01_rmd, including processed datasets, statistical results, tables, and figures.
R
Contains project-level R scripts used to support the analysis workflow, including configuration, project initialisation, and reusable helper functions.
  • config.R defines project-wide settings, parameters, and other configuration options used across analyses.
  • init_project.R initialises the analysis environment and loads the required project settings and supporting scripts.
  • utils.R contains reusable utility functions shared across multiple R Markdown files.
Separating these supporting scripts from the main analysis files helps maintain a consistent and reproducible workflow across analyses.
.here
The .here file defines the project root for the here R package. This allows file paths to be specified relative to the project root rather than using machine-specific absolute paths, improving portability and reproducibility.
.Rproj
The .Rproj file defines the corresponding RStudio project. Opening this file provides a consistent project environment and ensures that the analyses are run from the appropriate project directory.
Note on table numbering and order
The numbering and order of tables generated within the analysis scripts do not necessarily correspond to those of the supplementary tables submitted with the manuscript.
In the code repository, tables are organised according to the analytical workflow and their direct relationship to individual analyses. In the submitted Supplementary Information, tables are renumbered and ordered according to their sequence in the manuscript.
About
R scripts used for data processing, statistical analysis and visualisation in the BioNI wheat study.
Topics
bnimetabolomicsnitrificationsoil-microbiologywheat
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
BioNI Analysis Scripts
This repository contains the R scripts used for data analysis and figure generation in the manuscript.
The analyses are organised into three main project folders according to the corresponding figures:
  • 01_BNI_approaches_and_plant_traits contains the analyses and plotting scripts for Figures 1 and 2.
  • 02_root_exudate_metabolomics contains the analyses and plotting scripts for Figure 3.
  • 03_sequencing_analysis contains the analyses and plotting scripts for Figure 4.
Project structure
Each project follows a consistent directory structure:
00_input/
01_rmd/
02_docs/
03_analysis/
R/
.here
*.Rproj

00_input
Contains the input data required for the analyses, including processed experimental data, metadata, and other analysis-ready datasets.
01_rmd
Contains the main R Markdown (.Rmd) files used to run the analyses, together with the corresponding rendered HTML files for convenient viewing of the analysis workflow and outputs.
02_docs
Contains supporting documents where necessary.
03_analysis
Contains intermediate and final outputs generated by the workflows in 01_rmd, including processed datasets, statistical results, tables, and figures.
R
Contains project-level R scripts used to support the analysis workflow, including configuration, project initialisation, and reusable helper functions.
  • config.R defines project-wide settings, parameters, and other configuration options used across analyses.
  • init_project.R initialises the analysis environment and loads the required project settings and supporting scripts.
  • utils.R contains reusable utility functions shared across multiple R Markdown files.
Separating these supporting scripts from the main analysis files helps maintain a consistent and reproducible workflow across analyses.
.here
The .here file defines the project root for the here R package. This allows file paths to be specified relative to the project root rather than using machine-specific absolute paths, improving portability and reproducibility.
.Rproj
The .Rproj file defines the corresponding RStudio project. Opening this file provides a consistent project environment and ensures that the analyses are run from the appropriate project directory.
Note on table numbering and order
The numbering and order of tables generated within the analysis scripts do not necessarily correspond to those of the supplementary tables submitted with the manuscript.
In the code repository, tables are organised according to the analytical workflow and their direct relationship to individual analyses. In the submitted Supplementary Information, tables are renumbered and ordered according to their sequence in the manuscript.
About
R scripts used for data processing, statistical analysis and visualisation in the BioNI wheat study.
Topics
bnimetabolomicsnitrificationsoil-microbiologywheat
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
BioNI Analysis Scripts
This repository contains the R scripts used for data analysis and figure generation in the manuscript.
The analyses are organised into three main project folders according to the corresponding figures:
  • 01_BNI_approaches_and_plant_traits contains the analyses and plotting scripts for Figures 1 and 2.
  • 02_root_exudate_metabolomics contains the analyses and plotting scripts for Figure 3.
  • 03_sequencing_analysis contains the analyses and plotting scripts for Figure 4.
Project structure
Each project follows a consistent directory structure:
00_input/
01_rmd/
02_docs/
03_analysis/
R/
.here
*.Rproj

00_input
Contains the input data required for the analyses, including processed experimental data, metadata, and other analysis-ready datasets.
01_rmd
Contains the main R Markdown (.Rmd) files used to run the analyses, together with the corresponding rendered HTML files for convenient viewing of the analysis workflow and outputs.
02_docs
Contains supporting documents where necessary.
03_analysis
Contains intermediate and final outputs generated by the workflows in 01_rmd, including processed datasets, statistical results, tables, and figures.
R
Contains project-level R scripts used to support the analysis workflow, including configuration, project initialisation, and reusable helper functions.
  • config.R defines project-wide settings, parameters, and other configuration options used across analyses.
  • init_project.R initialises the analysis environment and loads the required project settings and supporting scripts.
  • utils.R contains reusable utility functions shared across multiple R Markdown files.
Separating these supporting scripts from the main analysis files helps maintain a consistent and reproducible workflow across analyses.
.here
The .here file defines the project root for the here R package. This allows file paths to be specified relative to the project root rather than using machine-specific absolute paths, improving portability and reproducibility.
.Rproj
The .Rproj file defines the corresponding RStudio project. Opening this file provides a consistent project environment and ensures that the analyses are run from the appropriate project directory.
Note on table numbering and order
The numbering and order of tables generated within the analysis scripts do not necessarily correspond to those of the supplementary tables submitted with the manuscript.
In the code repository, tables are organised according to the analytical workflow and their direct relationship to individual analyses. In the submitted Supplementary Information, tables are renumbered and ordered according to their sequence in the manuscript.
About
R scripts used for data processing, statistical analysis and visualisation in the BioNI wheat study.
Topics
bnimetabolomicsnitrificationsoil-microbiologywheat
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
BioNI Analysis Scripts
This repository contains the R scripts used for data analysis and figure generation in the manuscript.
The analyses are organised into three main project folders according to the corresponding figures:
  • 01_BNI_approaches_and_plant_traits contains the analyses and plotting scripts for Figures 1 and 2.
  • 02_root_exudate_metabolomics contains the analyses and plotting scripts for Figure 3.
  • 03_sequencing_analysis contains the analyses and plotting scripts for Figure 4.
Project structure
Each project follows a consistent directory structure:
00_input/
01_rmd/
02_docs/
03_analysis/
R/
.here
*.Rproj

00_input
Contains the input data required for the analyses, including processed experimental data, metadata, and other analysis-ready datasets.
01_rmd
Contains the main R Markdown (.Rmd) files used to run the analyses, together with the corresponding rendered HTML files for convenient viewing of the analysis workflow and outputs.
02_docs
Contains supporting documents where necessary.
03_analysis
Contains intermediate and final outputs generated by the workflows in 01_rmd, including processed datasets, statistical results, tables, and figures.
R
Contains project-level R scripts used to support the analysis workflow, including configuration, project initialisation, and reusable helper functions.
  • config.R defines project-wide settings, parameters, and other configuration options used across analyses.
  • init_project.R initialises the analysis environment and loads the required project settings and supporting scripts.
  • utils.R contains reusable utility functions shared across multiple R Markdown files.
Separating these supporting scripts from the main analysis files helps maintain a consistent and reproducible workflow across analyses.
.here
The .here file defines the project root for the here R package. This allows file paths to be specified relative to the project root rather than using machine-specific absolute paths, improving portability and reproducibility.
.Rproj
The .Rproj file defines the corresponding RStudio project. Opening this file provides a consistent project environment and ensures that the analyses are run from the appropriate project directory.
Note on table numbering and order
The numbering and order of tables generated within the analysis scripts do not necessarily correspond to those of the supplementary tables submitted with the manuscript.
In the code repository, tables are organised according to the analytical workflow and their direct relationship to individual analyses. In the submitted Supplementary Information, tables are renumbered and ordered according to their sequence in the manuscript.
About
R scripts used for data processing, statistical analysis and visualisation in the BioNI wheat study.
Topics
bnimetabolomicsnitrificationsoil-microbiologywheat
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
BioNI Analysis Scripts
This repository contains the R scripts used for data analysis and figure generation in the manuscript.
The analyses are organised into three main project folders according to the corresponding figures:
  • 01_BNI_approaches_and_plant_traits contains the analyses and plotting scripts for Figures 1 and 2.
  • 02_root_exudate_metabolomics contains the analyses and plotting scripts for Figure 3.
  • 03_sequencing_analysis contains the analyses and plotting scripts for Figure 4.
Project structure
Each project follows a consistent directory structure:
00_input/
01_rmd/
02_docs/
03_analysis/
R/
.here
*.Rproj

00_input
Contains the input data required for the analyses, including processed experimental data, metadata, and other analysis-ready datasets.
01_rmd
Contains the main R Markdown (.Rmd) files used to run the analyses, together with the corresponding rendered HTML files for convenient viewing of the analysis workflow and outputs.
02_docs
Contains supporting documents where necessary.
03_analysis
Contains intermediate and final outputs generated by the workflows in 01_rmd, including processed datasets, statistical results, tables, and figures.
R
Contains project-level R scripts used to support the analysis workflow, including configuration, project initialisation, and reusable helper functions.
  • config.R defines project-wide settings, parameters, and other configuration options used across analyses.
  • init_project.R initialises the analysis environment and loads the required project settings and supporting scripts.
  • utils.R contains reusable utility functions shared across multiple R Markdown files.
Separating these supporting scripts from the main analysis files helps maintain a consistent and reproducible workflow across analyses.
.here
The .here file defines the project root for the here R package. This allows file paths to be specified relative to the project root rather than using machine-specific absolute paths, improving portability and reproducibility.
.Rproj
The .Rproj file defines the corresponding RStudio project. Opening this file provides a consistent project environment and ensures that the analyses are run from the appropriate project directory.
Note on table numbering and order
The numbering and order of tables generated within the analysis scripts do not necessarily correspond to those of the supplementary tables submitted with the manuscript.
In the code repository, tables are organised according to the analytical workflow and their direct relationship to individual analyses. In the submitted Supplementary Information, tables are renumbered and ordered according to their sequence in the manuscript.
About
R scripts used for data processing, statistical analysis and visualisation in the BioNI wheat study.
Topics
bnimetabolomicsnitrificationsoil-microbiologywheat
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
BioNI Analysis Scripts
This repository contains the R scripts used for data analysis and figure generation in the manuscript.
The analyses are organised into three main project folders according to the corresponding figures:
  • 01_BNI_approaches_and_plant_traits contains the analyses and plotting scripts for Figures 1 and 2.
  • 02_root_exudate_metabolomics contains the analyses and plotting scripts for Figure 3.
  • 03_sequencing_analysis contains the analyses and plotting scripts for Figure 4.
Project structure
Each project follows a consistent directory structure:
00_input/
01_rmd/
02_docs/
03_analysis/
R/
.here
*.Rproj

00_input
Contains the input data required for the analyses, including processed experimental data, metadata, and other analysis-ready datasets.
01_rmd
Contains the main R Markdown (.Rmd) files used to run the analyses, together with the corresponding rendered HTML files for convenient viewing of the analysis workflow and outputs.
02_docs
Contains supporting documents where necessary.
03_analysis
Contains intermediate and final outputs generated by the workflows in 01_rmd, including processed datasets, statistical results, tables, and figures.
R
Contains project-level R scripts used to support the analysis workflow, including configuration, project initialisation, and reusable helper functions.
  • config.R defines project-wide settings, parameters, and other configuration options used across analyses.
  • init_project.R initialises the analysis environment and loads the required project settings and supporting scripts.
  • utils.R contains reusable utility functions shared across multiple R Markdown files.
Separating these supporting scripts from the main analysis files helps maintain a consistent and reproducible workflow across analyses.
.here
The .here file defines the project root for the here R package. This allows file paths to be specified relative to the project root rather than using machine-specific absolute paths, improving portability and reproducibility.
.Rproj
The .Rproj file defines the corresponding RStudio project. Opening this file provides a consistent project environment and ensures that the analyses are run from the appropriate project directory.
Note on table numbering and order
The numbering and order of tables generated within the analysis scripts do not necessarily correspond to those of the supplementary tables submitted with the manuscript.
In the code repository, tables are organised according to the analytical workflow and their direct relationship to individual analyses. In the submitted Supplementary Information, tables are renumbered and ordered according to their sequence in the manuscript.
About
R scripts used for data processing, statistical analysis and visualisation in the BioNI wheat study.
Topics
bnimetabolomicsnitrificationsoil-microbiologywheat
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages