{"id":49,"date":"2026-08-23T15:37:07","date_gmt":"2026-08-23T15:37:07","guid":{"rendered":"https:\/\/qoy.vxf.mybluehost.me\/website_11aa7f22\/tutorial\/"},"modified":"2026-09-17T04:59:12","modified_gmt":"2026-09-17T04:59:12","slug":"tutorial","status":"publish","type":"page","link":"https:\/\/aquaphotomics.com\/software\/aquagrammar\/tutorial\/","title":{"rendered":"Tutorial"},"content":{"rendered":"\r\n<p class=\"wp-block-paragraph\">This is the slow version. Getting started gets you a chart in a few minutes; this page explains what you are doing at each step, so that the chart means something when it appears.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Work with <strong>Demo 1 \u2014 Natural Systems<\/strong>. It is bundled, so nothing can go wrong that you cannot undo by starting over.<\/p>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"what-you-will-be-able-to-do\">What you will be able to do<\/h2>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li>Produce a Classic-12 Aquagram\u00ae from a MicroNIR file<\/li>\r\n\r\n\r\n<li>Explain what SNV, standardization, and repeat averaging did to your data<\/li>\r\n\r\n\r\n<li>Decide when to use Average, Add, or Subtract<\/li>\r\n\r\n\r\n<li>Read the chart without over-claiming what it shows<\/li>\r\n\r\n\r\n<li>Export results in a form you can use elsewhere<\/li>\r\n\r\n<\/ul>\r\n\r\n\r\n<a id=\"step-1\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"step-1-%c2%b7-open-a-file\">Step 1 \u00b7 Open a file<\/h2>\r\n\r\n\r\n<figure class=\"app-video\"><div class=\"app-video__frame\"><iframe src=\"https:\/\/www.youtube-nocookie.com\/embed\/qDxTKhdIjzU?rel=0\" title=\"Step 1 \u00b7 Open a file \u2014 40 seconds.\" loading=\"lazy\" referrerpolicy=\"strict-origin-when-cross-origin\" allow=\"accelerometer; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/div><figcaption>Step 1 \u00b7 Open a file \u2014 40 seconds.<\/figcaption><\/figure>\r\n\r\n\r\n<figure class=\"wp-block-image app-figure\"><img decoding=\"async\" loading=\"lazy\" src=\"\/software\/aquagrammar\/wp-content\/themes\/aquagrammar-help\/assets\/images\/aquagrammar-open-file.png\" alt=\"The Open a file screen: three cards for your own file, Demo 1, and Demo 2, with the four workflow steps down the left.\"\/><\/figure>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Select <strong>Open Demo 1<\/strong>. The file loads and AquaGrammar moves to step 2.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\"><strong>What just happened.<\/strong> AquaGrammar read a spreadsheet of spectra. Each row is one scan: a sample name, then an absorbance value at each wavelength. Nothing has been altered yet.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Notice the four steps down the left. They stay visible the whole time, and completed ones get a tick. You can click back to any of them without losing your work.<\/p>\r\n\r\n\r\n<a id=\"step-2\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"step-2-%c2%b7-select-sample-groups\">Step 2 \u00b7 Select sample groups<\/h2>\r\n\r\n\r\n<figure class=\"app-video\"><div class=\"app-video__frame\"><iframe src=\"https:\/\/www.youtube-nocookie.com\/embed\/skzXx5vqsJQ?rel=0\" title=\"Step 2 \u00b7 Select sample groups \u2014 41 seconds.\" loading=\"lazy\" referrerpolicy=\"strict-origin-when-cross-origin\" allow=\"accelerometer; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/div><figcaption>Step 2 \u00b7 Select sample groups \u2014 41 seconds.<\/figcaption><\/figure>\r\n\r\n\r\n<figure class=\"wp-block-image app-figure\"><img decoding=\"async\" loading=\"lazy\" src=\"\/software\/aquagrammar\/wp-content\/themes\/aquagrammar-help\/assets\/images\/aquagrammar-select-groups-cards.png\" alt=\"The Select sample groups screen with several groups ticked and the selected-count summary visible.\"\/><\/figure>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Demo 1 contains nine groups. Each shows a repeat count: <code>Stone1 (n=15)<\/code> means Stone1 was scanned fifteen times.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\"><strong>Tick Stone1, Stone2 and Stone3.<\/strong> Leave the rest unticked \u2014 they will be excluded entirely.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\"><strong>Why groups matter.<\/strong> A single scan carries measurement noise. Scanning the same sample repeatedly and averaging those repeats is what makes the result worth looking at. AquaGrammar does that averaging for you, but only within each group, so the groups must be right before you continue.<\/p>\r\n\r\n\r\n<h3 class=\"wp-block-heading\" id=\"choosing-the-snv-range\">Choosing the SNV range<\/h3>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Below the list, choose <strong>1st overtone 1300\u20131600<\/strong>.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">The twelve Classic-12 coordinates all sit between 1342 nm and 1512 nm \u2014 that is, inside the 1st overtone band. Normalizing over that range means each spectrum is scaled by the region you are about to plot, rather than by wavelengths that never reach the chart. <strong>Full range<\/strong> and <strong>Combination 1100\u20131300<\/strong> are available for comparison work.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Select <strong>Continue to row processing<\/strong>.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\"><strong>What just happened.<\/strong> Three things, in order, with no options to set:<\/p>\r\n\r\n\r\n<ol class=\"wp-block-list\">\r\n<li><strong>SNV<\/strong> was applied to each selected scan over your chosen range. This removes differences in overall brightness between scans, so that scans can be compared by shape rather than by level.<\/li>\r\n\r\n\r\n<li><strong>Standardization<\/strong> put every wavelength on the same footing across every scan in the file, as <code>(value \u2212 mean) \/ SD<\/code>.<\/li>\r\n\r\n\r\n<li><strong>Repeat averaging<\/strong> collapsed each group&#039;s repeats into one row.<\/li>\r\n\r\n<\/ol>\r\n\r\n\r\n<a id=\"step-3\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"step-3-%c2%b7-process-rows\">Step 3 \u00b7 Process rows<\/h2>\r\n\r\n\r\n<figure class=\"app-video\"><div class=\"app-video__frame\"><iframe src=\"https:\/\/www.youtube-nocookie.com\/embed\/PXYQUSseSbU?rel=0\" title=\"Step 3 \u00b7 Process rows \u2014 45 seconds.\" loading=\"lazy\" referrerpolicy=\"strict-origin-when-cross-origin\" allow=\"accelerometer; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/div><figcaption>Step 3 \u00b7 Process rows \u2014 45 seconds.<\/figcaption><\/figure>\r\n\r\n\r\n<figure class=\"wp-block-image app-figure\"><img decoding=\"async\" loading=\"lazy\" src=\"\/software\/aquagrammar\/wp-content\/themes\/aquagrammar-help\/assets\/images\/aquagrammar-process-rows-selected.png\" alt=\"The Process rows screen: Inputs for Aquagram on the left with an Average row created, Operation panel on the right.\"\/><\/figure>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">The left panel lists your three prepared groups under *Original groups \u00b7 SNV applied*, each with a coloured dot \u2014 the colour its line will take.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">You could tick all three now and plot them. Instead, try an operation first, so you can see where processed rows come from.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">On the right, with <strong>Average<\/strong> selected, tick <strong>Stone1<\/strong> and <strong>Stone2<\/strong>, then select <strong>Create average row<\/strong>. A new row appears on the left under *Processed results*, named after what made it.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\"><strong>The three operations<\/strong><\/p>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li><strong>Average<\/strong> \u2014 the mean of two or more groups. Use it when the groups are replicates of the same thing and you want one representative line.<\/li>\r\n\r\n\r\n<li><strong>Add<\/strong> \u2014 the sum of two or more groups.<\/li>\r\n\r\n\r\n<li><strong>Subtract<\/strong> \u2014 pick any number of groups to adjust, plus one baseline, and get one result per adjusted group. Use it to ask *how does each of these differ from that reference?* Subtracting a group from itself gives zero, which is a useful sanity check.<\/li>\r\n\r\n<\/ul>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">A processed row is not a dead end: rename it with the pencil, delete it with the \u00d7, or use it as an input to another operation.<\/p>\r\n\r\n\r\n<a id=\"step-4\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"step-4-%c2%b7-read-the-aquagram\">Step 4 \u00b7 Read the Aquagram\u00ae<\/h2>\r\n\r\n\r\n<figure class=\"app-video\"><div class=\"app-video__frame\"><iframe src=\"https:\/\/www.youtube-nocookie.com\/embed\/aGs7Ez-Wo9w?rel=0\" title=\"Step 4 \u00b7 Read the Aquagram\u00ae \u2014 44 seconds.\" loading=\"lazy\" referrerpolicy=\"strict-origin-when-cross-origin\" allow=\"accelerometer; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/div><figcaption>Step 4 \u00b7 Read the Aquagram\u00ae \u2014 44 seconds.<\/figcaption><\/figure>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Tick the rows you want to plot \u2014 try Stone1, Stone2 and Stone3 \u2014 then select <strong>Generate Classic-12 Aquagram\u00ae<\/strong>.<\/p>\r\n\r\n\r\n<figure class=\"wp-block-image app-figure\"><img decoding=\"async\" loading=\"lazy\" src=\"\/software\/aquagrammar\/wp-content\/themes\/aquagrammar-help\/assets\/images\/aquagrammar-results.png\" alt=\"The results screen: a white radar chart with three coloured lines, a legend beneath, and the export buttons.\"\/><\/figure>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Each ticked row is now one line. Twelve spokes radiate from the centre, one per Classic-12 coordinate, each labelled with its wavelength and what that wavelength is associated with \u2014 for example *1412nm (S0 free OH)*.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\"><strong>Reading it.<\/strong> Points further from the centre mean a higher standardized value at that coordinate. The useful question is almost never &quot;what is this line&#039;s absolute value&quot; but &quot;where do these lines differ from each other&quot;. That is what the shape is for.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Try these:<\/p>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li><strong>Select a legend entry<\/strong> to hide its line, then show it again. Comparing two lines is easier with the third out of the way.<\/li>\r\n\r\n\r\n<li><strong>Zoom<\/strong> with \u2212 and +. Above 100% you can drag the chart to pan.<\/li>\r\n\r\n\r\n<li><strong>Hover a line<\/strong> to read the exact coordinate and value under the cursor.<\/li>\r\n\r\n\r\n<li><strong>View overall mean table<\/strong> shows the twelve values averaged across the lines you plotted.<\/li>\r\n\r\n<\/ul>\r\n\r\n\r\n<p class=\"wp-block-paragraph\"><strong>Interpreting responsibly.<\/strong> Describe what differs and where. An Aquagram\u00ae does not, by itself, identify a disease, prove a treatment worked, or establish anything about an individual. It is a way of seeing a pattern; the meaning comes from the experiment behind it.<\/p>\r\n\r\n\r\n<a id=\"export\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"exporting\">Exporting<\/h2>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Four formats, and the difference matters:<\/p>\r\n\r\n\r\n<figure class=\"wp-block-table\"><table><thead><tr><th>Format<\/th><th>What you get<\/th><th>Use it to<\/th><\/tr><\/thead><tbody><tr><td><strong>XLSX<\/strong>, <strong>CSV<\/strong><\/td><td>One column per plotted line: the WAMACS wavelength, then each line&#039;s values<\/td><td>Rebuild the chart in your own tools, or check the numbers<\/td><\/tr><tr><td><strong>PNG<\/strong>, <strong>JPG<\/strong><\/td><td>The chart image together with its legend<\/td><td>Drop into a slide or a document<\/td><\/tr><\/tbody><\/table><\/figure>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">These four are the only export formats in Preview.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">To start over, click an earlier step in the left rail, or open a different file. Preview does not save projects \u2014 when you open a new file, the previous session is replaced.<\/p>\r\n\r\n\r\n<a id=\"knowledge-check\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"check-yourself\">Check yourself<\/h2>\r\n\r\n\r\n<ol class=\"wp-block-list\">\r\n<li>What are the four steps, and what does each one produce?<\/li>\r\n\r\n\r\n<li>Why does AquaGrammar average repeats within a group rather than across all your scans?<\/li>\r\n\r\n\r\n<li>Why is 1st overtone the suggested SNV range for Classic-12 work?<\/li>\r\n\r\n\r\n<li>Average needs at least two groups. What does Subtract need?<\/li>\r\n\r\n\r\n<li>Which exports let you rebuild the chart yourself, and which give you a picture?<\/li>\r\n\r\n\r\n<li>Someone shows you an Aquagram\u00ae and says it proves a sample is healthy. What is wrong with that claim?<\/li>\r\n\r\n<\/ol>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"next\">Next<\/h2>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li><a href=\"\/software\/aquagrammar\/user-guide\/\">How AquaGrammar works<\/a> \u2014 what each processing step does<\/li>\r\n\r\n\r\n<li><a href=\"\/software\/aquagrammar\/glossary\/\">Glossary<\/a> \u2014 the words used here<\/li>\r\n\r\n\r\n<li><a href=\"\/software\/aquagrammar\/troubleshooting\/\">Troubleshooting<\/a> \u2014 if something behaved unexpectedly<\/li>\r\n\r\n<\/ul>\r\n","protected":false},"excerpt":{"rendered":"<p>This is the slow version. Getting started gets you a chart in a few minutes; this page explains what you are doing at each step, so that the chart means something when it appears. Work with Demo 1 \u2014 Natural Systems. It is bundled, so nothing can go wrong that you cannot undo by starting [&hellip;]<\/p>\n","protected":false},"author":0,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"nf_dc_page":"","om_disable_all_campaigns":false,"_monsterinsights_skip_tracking":false,"footnotes":""},"class_list":["post-49","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Tutorial - AquaGrammar<\/title>\n<meta name=\"description\" content=\"A slower, explained walkthrough of all four AquaGrammar steps, with a short video for each: open a file, select groups, process rows, read the Aquagram.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/aquaphotomics.com\/software\/aquagrammar\/tutorial\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tutorial - 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