").addClass(errClass).css("position", "absolute")
+ .css("top", el.offsetTop)
+ .css("left", el.offsetLeft)
+ // setting width can push out the page size, forcing otherwise
+ // unnecessary scrollbars to appear and making it impossible for
+ // the element to shrink; so use max-width instead
+ .css("maxWidth", el.offsetWidth)
+ .css("height", el.offsetHeight);
+ errorDiv.text(err.message);
+ $el.after(errorDiv);
+
+ // Really dumb way to keep the size/position of the error in sync with
+ // the parent element as the window is resized or whatever.
+ var intId = setInterval(function() {
+ if (!errorDiv[0].parentElement) {
+ clearInterval(intId);
+ return;
+ }
+ errorDiv
+ .css("top", el.offsetTop)
+ .css("left", el.offsetLeft)
+ .css("maxWidth", el.offsetWidth)
+ .css("height", el.offsetHeight);
+ }, 500);
+ }
+ }
+ },
+ clearError: function(el) {
+ var $el = $(el);
+ var display = $el.data("restore-display-mode");
+ $el.data("restore-display-mode", null);
+
+ if (display === "inline" || display === "inline-block") {
+ if (display)
+ $el.css("display", display);
+ $(el.nextSibling).filter(".htmlwidgets-error").remove();
+ } else if (display === "block"){
+ $el.css("visibility", "inherit");
+ $(el.nextSibling).filter(".htmlwidgets-error").remove();
+ }
+ },
+ sizing: {}
+ };
+
+ // Called by widget bindings to register a new type of widget. The definition
+ // object can contain the following properties:
+ // - name (required) - A string indicating the binding name, which will be
+ // used by default as the CSS classname to look for.
+ // - initialize (optional) - A function(el) that will be called once per
+ // widget element; if a value is returned, it will be passed as the third
+ // value to renderValue.
+ // - renderValue (required) - A function(el, data, initValue) that will be
+ // called with data. Static contexts will cause this to be called once per
+ // element; Shiny apps will cause this to be called multiple times per
+ // element, as the data changes.
+ window.HTMLWidgets.widget = function(definition) {
+ if (!definition.name) {
+ throw new Error("Widget must have a name");
+ }
+ if (!definition.type) {
+ throw new Error("Widget must have a type");
+ }
+ // Currently we only support output widgets
+ if (definition.type !== "output") {
+ throw new Error("Unrecognized widget type '" + definition.type + "'");
+ }
+ // TODO: Verify that .name is a valid CSS classname
+
+ // Support new-style instance-bound definitions. Old-style class-bound
+ // definitions have one widget "object" per widget per type/class of
+ // widget; the renderValue and resize methods on such widget objects
+ // take el and instance arguments, because the widget object can't
+ // store them. New-style instance-bound definitions have one widget
+ // object per widget instance; the definition that's passed in doesn't
+ // provide renderValue or resize methods at all, just the single method
+ // factory(el, width, height)
+ // which returns an object that has renderValue(x) and resize(w, h).
+ // This enables a far more natural programming style for the widget
+ // author, who can store per-instance state using either OO-style
+ // instance fields or functional-style closure variables (I guess this
+ // is in contrast to what can only be called C-style pseudo-OO which is
+ // what we required before).
+ if (definition.factory) {
+ definition = createLegacyDefinitionAdapter(definition);
+ }
+
+ if (!definition.renderValue) {
+ throw new Error("Widget must have a renderValue function");
+ }
+
+ // For static rendering (non-Shiny), use a simple widget registration
+ // scheme. We also use this scheme for Shiny apps/documents that also
+ // contain static widgets.
+ window.HTMLWidgets.widgets = window.HTMLWidgets.widgets || [];
+ // Merge defaults into the definition; don't mutate the original definition.
+ var staticBinding = extend({}, defaults, definition);
+ overrideMethod(staticBinding, "find", function(superfunc) {
+ return function(scope) {
+ var results = superfunc(scope);
+ // Filter out Shiny outputs, we only want the static kind
+ return filterByClass(results, "html-widget-output", false);
+ };
+ });
+ window.HTMLWidgets.widgets.push(staticBinding);
+
+ if (shinyMode) {
+ // Shiny is running. Register the definition with an output binding.
+ // The definition itself will not be the output binding, instead
+ // we will make an output binding object that delegates to the
+ // definition. This is because we foolishly used the same method
+ // name (renderValue) for htmlwidgets definition and Shiny bindings
+ // but they actually have quite different semantics (the Shiny
+ // bindings receive data that includes lots of metadata that it
+ // strips off before calling htmlwidgets renderValue). We can't
+ // just ignore the difference because in some widgets it's helpful
+ // to call this.renderValue() from inside of resize(), and if
+ // we're not delegating, then that call will go to the Shiny
+ // version instead of the htmlwidgets version.
+
+ // Merge defaults with definition, without mutating either.
+ var bindingDef = extend({}, defaults, definition);
+
+ // This object will be our actual Shiny binding.
+ var shinyBinding = new Shiny.OutputBinding();
+
+ // With a few exceptions, we'll want to simply use the bindingDef's
+ // version of methods if they are available, otherwise fall back to
+ // Shiny's defaults. NOTE: If Shiny's output bindings gain additional
+ // methods in the future, and we want them to be overrideable by
+ // HTMLWidget binding definitions, then we'll need to add them to this
+ // list.
+ delegateMethod(shinyBinding, bindingDef, "getId");
+ delegateMethod(shinyBinding, bindingDef, "onValueChange");
+ delegateMethod(shinyBinding, bindingDef, "onValueError");
+ delegateMethod(shinyBinding, bindingDef, "renderError");
+ delegateMethod(shinyBinding, bindingDef, "clearError");
+ delegateMethod(shinyBinding, bindingDef, "showProgress");
+
+ // The find, renderValue, and resize are handled differently, because we
+ // want to actually decorate the behavior of the bindingDef methods.
+
+ shinyBinding.find = function(scope) {
+ var results = bindingDef.find(scope);
+
+ // Only return elements that are Shiny outputs, not static ones
+ var dynamicResults = results.filter(".html-widget-output");
+
+ // It's possible that whatever caused Shiny to think there might be
+ // new dynamic outputs, also caused there to be new static outputs.
+ // Since there might be lots of different htmlwidgets bindings, we
+ // schedule execution for later--no need to staticRender multiple
+ // times.
+ if (results.length !== dynamicResults.length)
+ scheduleStaticRender();
+
+ return dynamicResults;
+ };
+
+ // Wrap renderValue to handle initialization, which unfortunately isn't
+ // supported natively by Shiny at the time of this writing.
+
+ shinyBinding.renderValue = function(el, data) {
+ Shiny.renderDependencies(data.deps);
+ // Resolve strings marked as javascript literals to objects
+ if (!(data.evals instanceof Array)) data.evals = [data.evals];
+ for (var i = 0; data.evals && i < data.evals.length; i++) {
+ window.HTMLWidgets.evaluateStringMember(data.x, data.evals[i]);
+ }
+ if (!bindingDef.renderOnNullValue) {
+ if (data.x === null) {
+ el.style.visibility = "hidden";
+ return;
+ } else {
+ el.style.visibility = "inherit";
+ }
+ }
+ if (!elementData(el, "initialized")) {
+ initSizing(el);
+
+ elementData(el, "initialized", true);
+ if (bindingDef.initialize) {
+ var result = bindingDef.initialize(el, el.offsetWidth,
+ el.offsetHeight);
+ elementData(el, "init_result", result);
+ }
+ }
+ bindingDef.renderValue(el, data.x, elementData(el, "init_result"));
+ evalAndRun(data.jsHooks.render, elementData(el, "init_result"), [el, data.x]);
+ };
+
+ // Only override resize if bindingDef implements it
+ if (bindingDef.resize) {
+ shinyBinding.resize = function(el, width, height) {
+ // Shiny can call resize before initialize/renderValue have been
+ // called, which doesn't make sense for widgets.
+ if (elementData(el, "initialized")) {
+ bindingDef.resize(el, width, height, elementData(el, "init_result"));
+ }
+ };
+ }
+
+ Shiny.outputBindings.register(shinyBinding, bindingDef.name);
+ }
+ };
+
+ var scheduleStaticRenderTimerId = null;
+ function scheduleStaticRender() {
+ if (!scheduleStaticRenderTimerId) {
+ scheduleStaticRenderTimerId = setTimeout(function() {
+ scheduleStaticRenderTimerId = null;
+ window.HTMLWidgets.staticRender();
+ }, 1);
+ }
+ }
+
+ // Render static widgets after the document finishes loading
+ // Statically render all elements that are of this widget's class
+ window.HTMLWidgets.staticRender = function() {
+ var bindings = window.HTMLWidgets.widgets || [];
+ forEach(bindings, function(binding) {
+ var matches = binding.find(document.documentElement);
+ forEach(matches, function(el) {
+ var sizeObj = initSizing(el, binding);
+
+ if (hasClass(el, "html-widget-static-bound"))
+ return;
+ el.className = el.className + " html-widget-static-bound";
+
+ var initResult;
+ if (binding.initialize) {
+ initResult = binding.initialize(el,
+ sizeObj ? sizeObj.getWidth() : el.offsetWidth,
+ sizeObj ? sizeObj.getHeight() : el.offsetHeight
+ );
+ elementData(el, "init_result", initResult);
+ }
+
+ if (binding.resize) {
+ var lastSize = {
+ w: sizeObj ? sizeObj.getWidth() : el.offsetWidth,
+ h: sizeObj ? sizeObj.getHeight() : el.offsetHeight
+ };
+ var resizeHandler = function(e) {
+ var size = {
+ w: sizeObj ? sizeObj.getWidth() : el.offsetWidth,
+ h: sizeObj ? sizeObj.getHeight() : el.offsetHeight
+ };
+ if (size.w === 0 && size.h === 0)
+ return;
+ if (size.w === lastSize.w && size.h === lastSize.h)
+ return;
+ lastSize = size;
+ binding.resize(el, size.w, size.h, initResult);
+ };
+
+ on(window, "resize", resizeHandler);
+
+ // This is needed for cases where we're running in a Shiny
+ // app, but the widget itself is not a Shiny output, but
+ // rather a simple static widget. One example of this is
+ // an rmarkdown document that has runtime:shiny and widget
+ // that isn't in a render function. Shiny only knows to
+ // call resize handlers for Shiny outputs, not for static
+ // widgets, so we do it ourselves.
+ if (window.jQuery) {
+ window.jQuery(document).on(
+ "shown.htmlwidgets shown.bs.tab.htmlwidgets shown.bs.collapse.htmlwidgets",
+ resizeHandler
+ );
+ window.jQuery(document).on(
+ "hidden.htmlwidgets hidden.bs.tab.htmlwidgets hidden.bs.collapse.htmlwidgets",
+ resizeHandler
+ );
+ }
+
+ // This is needed for the specific case of ioslides, which
+ // flips slides between display:none and display:block.
+ // Ideally we would not have to have ioslide-specific code
+ // here, but rather have ioslides raise a generic event,
+ // but the rmarkdown package just went to CRAN so the
+ // window to getting that fixed may be long.
+ if (window.addEventListener) {
+ // It's OK to limit this to window.addEventListener
+ // browsers because ioslides itself only supports
+ // such browsers.
+ on(document, "slideenter", resizeHandler);
+ on(document, "slideleave", resizeHandler);
+ }
+ }
+
+ var scriptData = document.querySelector("script[data-for='" + el.id + "'][type='application/json']");
+ if (scriptData) {
+ var data = JSON.parse(scriptData.textContent || scriptData.text);
+ // Resolve strings marked as javascript literals to objects
+ if (!(data.evals instanceof Array)) data.evals = [data.evals];
+ for (var k = 0; data.evals && k < data.evals.length; k++) {
+ window.HTMLWidgets.evaluateStringMember(data.x, data.evals[k]);
+ }
+ binding.renderValue(el, data.x, initResult);
+ evalAndRun(data.jsHooks.render, initResult, [el, data.x]);
+ }
+ });
+ });
+
+ invokePostRenderHandlers();
+ }
+
+ // Wait until after the document has loaded to render the widgets.
+ if (document.addEventListener) {
+ document.addEventListener("DOMContentLoaded", function() {
+ document.removeEventListener("DOMContentLoaded", arguments.callee, false);
+ window.HTMLWidgets.staticRender();
+ }, false);
+ } else if (document.attachEvent) {
+ document.attachEvent("onreadystatechange", function() {
+ if (document.readyState === "complete") {
+ document.detachEvent("onreadystatechange", arguments.callee);
+ window.HTMLWidgets.staticRender();
+ }
+ });
+ }
+
+
+ window.HTMLWidgets.getAttachmentUrl = function(depname, key) {
+ // If no key, default to the first item
+ if (typeof(key) === "undefined")
+ key = 1;
+
+ var link = document.getElementById(depname + "-" + key + "-attachment");
+ if (!link) {
+ throw new Error("Attachment " + depname + "/" + key + " not found in document");
+ }
+ return link.getAttribute("href");
+ };
+
+ window.HTMLWidgets.dataframeToD3 = function(df) {
+ var names = [];
+ var length;
+ for (var name in df) {
+ if (df.hasOwnProperty(name))
+ names.push(name);
+ if (typeof(df[name]) !== "object" || typeof(df[name].length) === "undefined") {
+ throw new Error("All fields must be arrays");
+ } else if (typeof(length) !== "undefined" && length !== df[name].length) {
+ throw new Error("All fields must be arrays of the same length");
+ }
+ length = df[name].length;
+ }
+ var results = [];
+ var item;
+ for (var row = 0; row < length; row++) {
+ item = {};
+ for (var col = 0; col < names.length; col++) {
+ item[names[col]] = df[names[col]][row];
+ }
+ results.push(item);
+ }
+ return results;
+ };
+
+ window.HTMLWidgets.transposeArray2D = function(array) {
+ if (array.length === 0) return array;
+ var newArray = array[0].map(function(col, i) {
+ return array.map(function(row) {
+ return row[i]
+ })
+ });
+ return newArray;
+ };
+ // Split value at splitChar, but allow splitChar to be escaped
+ // using escapeChar. Any other characters escaped by escapeChar
+ // will be included as usual (including escapeChar itself).
+ function splitWithEscape(value, splitChar, escapeChar) {
+ var results = [];
+ var escapeMode = false;
+ var currentResult = "";
+ for (var pos = 0; pos < value.length; pos++) {
+ if (!escapeMode) {
+ if (value[pos] === splitChar) {
+ results.push(currentResult);
+ currentResult = "";
+ } else if (value[pos] === escapeChar) {
+ escapeMode = true;
+ } else {
+ currentResult += value[pos];
+ }
+ } else {
+ currentResult += value[pos];
+ escapeMode = false;
+ }
+ }
+ if (currentResult !== "") {
+ results.push(currentResult);
+ }
+ return results;
+ }
+ // Function authored by Yihui/JJ Allaire
+ window.HTMLWidgets.evaluateStringMember = function(o, member) {
+ var parts = splitWithEscape(member, '.', '\\');
+ for (var i = 0, l = parts.length; i < l; i++) {
+ var part = parts[i];
+ // part may be a character or 'numeric' member name
+ if (o !== null && typeof o === "object" && part in o) {
+ if (i == (l - 1)) { // if we are at the end of the line then evalulate
+ if (typeof o[part] === "string")
+ o[part] = eval("(" + o[part] + ")");
+ } else { // otherwise continue to next embedded object
+ o = o[part];
+ }
+ }
+ }
+ };
+
+ // Retrieve the HTMLWidget instance (i.e. the return value of an
+ // HTMLWidget binding's initialize() or factory() function)
+ // associated with an element, or null if none.
+ window.HTMLWidgets.getInstance = function(el) {
+ return elementData(el, "init_result");
+ };
+
+ // Finds the first element in the scope that matches the selector,
+ // and returns the HTMLWidget instance (i.e. the return value of
+ // an HTMLWidget binding's initialize() or factory() function)
+ // associated with that element, if any. If no element matches the
+ // selector, or the first matching element has no HTMLWidget
+ // instance associated with it, then null is returned.
+ //
+ // The scope argument is optional, and defaults to window.document.
+ window.HTMLWidgets.find = function(scope, selector) {
+ if (arguments.length == 1) {
+ selector = scope;
+ scope = document;
+ }
+
+ var el = scope.querySelector(selector);
+ if (el === null) {
+ return null;
+ } else {
+ return window.HTMLWidgets.getInstance(el);
+ }
+ };
+
+ // Finds all elements in the scope that match the selector, and
+ // returns the HTMLWidget instances (i.e. the return values of
+ // an HTMLWidget binding's initialize() or factory() function)
+ // associated with the elements, in an array. If elements that
+ // match the selector don't have an associated HTMLWidget
+ // instance, the returned array will contain nulls.
+ //
+ // The scope argument is optional, and defaults to window.document.
+ window.HTMLWidgets.findAll = function(scope, selector) {
+ if (arguments.length == 1) {
+ selector = scope;
+ scope = document;
+ }
+
+ var nodes = scope.querySelectorAll(selector);
+ var results = [];
+ for (var i = 0; i < nodes.length; i++) {
+ results.push(window.HTMLWidgets.getInstance(nodes[i]));
+ }
+ return results;
+ };
+
+ var postRenderHandlers = [];
+ function invokePostRenderHandlers() {
+ while (postRenderHandlers.length) {
+ var handler = postRenderHandlers.shift();
+ if (handler) {
+ handler();
+ }
+ }
+ }
+
+ // Register the given callback function to be invoked after the
+ // next time static widgets are rendered.
+ window.HTMLWidgets.addPostRenderHandler = function(callback) {
+ postRenderHandlers.push(callback);
+ };
+
+ // Takes a new-style instance-bound definition, and returns an
+ // old-style class-bound definition. This saves us from having
+ // to rewrite all the logic in this file to accomodate both
+ // types of definitions.
+ function createLegacyDefinitionAdapter(defn) {
+ var result = {
+ name: defn.name,
+ type: defn.type,
+ initialize: function(el, width, height) {
+ return defn.factory(el, width, height);
+ },
+ renderValue: function(el, x, instance) {
+ return instance.renderValue(x);
+ },
+ resize: function(el, width, height, instance) {
+ return instance.resize(width, height);
+ }
+ };
+
+ if (defn.find)
+ result.find = defn.find;
+ if (defn.renderError)
+ result.renderError = defn.renderError;
+ if (defn.clearError)
+ result.clearError = defn.clearError;
+
+ return result;
+ }
+})();
+
diff --git a/docs/assets/jquery-2.2.3/jquery.min.js b/docs/assets/jquery-2.2.3/jquery.min.js
new file mode 100644
index 0000000..b8c4187
--- /dev/null
+++ b/docs/assets/jquery-2.2.3/jquery.min.js
@@ -0,0 +1,4 @@
+/*! jQuery v2.2.3 | (c) jQuery Foundation | jquery.org/license */
+!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){var c=[],d=a.document,e=c.slice,f=c.concat,g=c.push,h=c.indexOf,i={},j=i.toString,k=i.hasOwnProperty,l={},m="2.2.3",n=function(a,b){return new n.fn.init(a,b)},o=/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,p=/^-ms-/,q=/-([\da-z])/gi,r=function(a,b){return b.toUpperCase()};n.fn=n.prototype={jquery:m,constructor:n,selector:"",length:0,toArray:function(){return e.call(this)},get:function(a){return null!=a?0>a?this[a+this.length]:this[a]:e.call(this)},pushStack:function(a){var b=n.merge(this.constructor(),a);return b.prevObject=this,b.context=this.context,b},each:function(a){return n.each(this,a)},map:function(a){return this.pushStack(n.map(this,function(b,c){return a.call(b,c,b)}))},slice:function(){return this.pushStack(e.apply(this,arguments))},first:function(){return this.eq(0)},last:function(){return this.eq(-1)},eq:function(a){var b=this.length,c=+a+(0>a?b:0);return this.pushStack(c>=0&&b>c?[this[c]]:[])},end:function(){return this.prevObject||this.constructor()},push:g,sort:c.sort,splice:c.splice},n.extend=n.fn.extend=function(){var a,b,c,d,e,f,g=arguments[0]||{},h=1,i=arguments.length,j=!1;for("boolean"==typeof g&&(j=g,g=arguments[h]||{},h++),"object"==typeof g||n.isFunction(g)||(g={}),h===i&&(g=this,h--);i>h;h++)if(null!=(a=arguments[h]))for(b in a)c=g[b],d=a[b],g!==d&&(j&&d&&(n.isPlainObject(d)||(e=n.isArray(d)))?(e?(e=!1,f=c&&n.isArray(c)?c:[]):f=c&&n.isPlainObject(c)?c:{},g[b]=n.extend(j,f,d)):void 0!==d&&(g[b]=d));return g},n.extend({expando:"jQuery"+(m+Math.random()).replace(/\D/g,""),isReady:!0,error:function(a){throw new Error(a)},noop:function(){},isFunction:function(a){return"function"===n.type(a)},isArray:Array.isArray,isWindow:function(a){return 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Biplots
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Ordination objects are best represented in biplots, which simultaneously display the projections of observations (points) and variables (arrows) over the same space. There are several options for creating biplots in R, starting with the readily available biplot function:
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biplot (prot1)
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Although there are several options for customizing this default biplot function, we recommend the use of the biplot2d3d package. This package wraps a lot of possibilities in R.
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library (biplot2d3d)
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The biplot2d3d package use functions of other packages to allow the customization of virtually all aspects of a biplot. Another important feature of this package is the creation of three-dimensional interactive biplots using the rgl package.
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Biplot 2D
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You can consult all tuning options available in the biplot_2d function by calling up the help file:
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?biplot_2d
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The default configuration will probably give you a much clearer picture than the biplot function, specially if your dataset contains more than 100 observations.
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biplot_2d (prot1)
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The default setting detaches the variables projections (arrows) and places them as a miniature in the bottom-right corner. In this format they may still be interpreted, much like the North when reading a map. Remember though: the more longer arrows you see, the less each one of them is reliable when comparing point values. Here, we were ‘lucky’ for getting two nearly orthogonal variables (CaO and MgO), which means, for instance, that those observations in the bottom-left corner are surely more calcareous than those in the top-right. See the Appendix section for more details.
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If detaching the arrows is not of your preference, you can disable this:
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biplot_2d (prot1,
+ detach_arrows = FALSE ,
+ output_type = "preview" )
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You can also visualize how the projection of points respond to a given typology (in this case, the chemical reference groups defined in previous studies).
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biplot_2d (prot1,
+ groups = factor_list$ ChemGroup,
+ output_type = "preview" )
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To get a prettier plot or match your research needs, you can play with the options given by the biplot_2d .
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biplot_2d (prot1,
+ groups = factor_list$ ChemGroup,
+ group_color = color_list$ ChemGroup,
+ group_label_cex = 0.6 ,
+ invert_coordinates = c (TRUE , TRUE ),
+ arrow_label_cex = 0.7 ,
+ test_text = prot1_tests$ text (prot1_tests),
+ test_cex = 0.8 ,
+ test_fig = c (0 , 0.5 , 0.65 , .99 ),
+ output_type = "preview" )
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+
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biplot_2d (prot1,
+ groups = factor_list$ ChemGroup,
+ group_color = color_list$ ChemGroup,
+ group_label_cex = 0 ,
+ group_star_cex = 0 ,
+ group_ellipse_cex = 0 ,
+ point_type = "label" ,
+ point_label = row.names (cleanAmphorae)[! isShipwreck],
+ point_label_cex = 0.5 ,
+ invert_coordinates = c (TRUE , TRUE ),
+ arrow_label_cex = 0.7 ,
+ test_text = prot1_tests$ text (prot1_tests),
+ test_cex = 0.8 ,
+ test_fig = c (0 , 0.5 , 0.65 , .99 ),
+ output_type = "preview" )
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It is also possible to save 2D biplots into various file formats (png, tiff, jpeg, eps):
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# better PNG version
+biplot_2d (prot1,
+ ordination_method = "PCA" ,
+ invert_coordinates = c (TRUE ,TRUE ),
+ grid_cex = 2.5 ,
+ ylim = c (- .1 ,.1 ),
+ point_type = "point" ,
+ groups = factor_list$ ChemGroup,
+ group_color = color_list$ ChemGroup,
+ group_label_cex = 1.5 ,
+ arrow_label_cex = 2 ,
+ arrow_cex = 0.2 ,
+ arrow_lwd = 2.5 ,
+ arrow_fig = c (.6 ,.95 ,0 ,.35 ),
+ subtitle_cex = 2.5 ,
+ test_text = prot1_tests$ text (prot1_tests),
+ test_fig = c (0 , 0.5 , 0.62 , .99 ),
+ test_cex = 2 ,
+ fitAnalysis_fig = c (0 ,.7 ,.05 ,.5 ),
+ # saving settings
+ file_name = "Prot1_Biplot2D" ,
+ directory = directories$ prot1,
+ width = 1000 , height = 1000 ,
+ output_type = "png" )
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Biplot 3D
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Most 2D options are also available when generating 3D biplots. Consult the help file for details.
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?biplot_3d
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biplot_3d (prot1,
+ ordination_method = "PCA" ,
+ groups = factor_list$ ChemGroup,
+ group_color = color_list$ ChemGroup,
+ point_type = "point" ,
+ group_representation = "stars" ,
+ star_centroid_radius = 0 ,
+ star_label_cex = .8 ,
+ test_text = prot1_tests$ text (prot1_tests),
+ test_cex = 1.25 ,
+ test_fig = c (0 , 0.5 , 0.65 , .99 ))
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You can save an animated GIF and a PNG snapshot using the animation function.
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biplot2d3d:: animation (directory = directories$ prot1,
+ file_name = "Prot1_Biplot3D" )
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You will need to install ImageMagick to be able to generate the GIF animation.
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In these images, you get what you would see when running the biplot_3d function in a regular R session.
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NOTE: Animated GIF will not be displayed in the pdf version of this document.
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