").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 rect = el.getBoundingClientRect();
+ var result = bindingDef.initialize(el, rect.width, rect.height);
+ 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);
+
+ var getSize = function(el) {
+ if (sizeObj) {
+ return {w: sizeObj.getWidth(), h: sizeObj.getHeight()}
+ } else {
+ var rect = el.getBoundingClientRect();
+ return {w: rect.width, h: rect.height}
+ }
+ };
+
+ if (hasClass(el, "html-widget-static-bound"))
+ return;
+ el.className = el.className + " html-widget-static-bound";
+
+ var initResult;
+ if (binding.initialize) {
+ var size = getSize(el);
+ initResult = binding.initialize(el, size.w, size.h);
+ elementData(el, "init_result", initResult);
+ }
+
+ if (binding.resize) {
+ var lastSize = getSize(el);
+ var resizeHandler = function(e) {
+ var size = getSize(el);
+ 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();
+ }
+
+
+ function has_jQuery3() {
+ if (!window.jQuery) {
+ return false;
+ }
+ var $version = window.jQuery.fn.jquery;
+ var $major_version = parseInt($version.split(".")[0]);
+ return $major_version >= 3;
+ }
+
+ /*
+ / Shiny 1.4 bumped jQuery from 1.x to 3.x which means jQuery's
+ / on-ready handler (i.e., $(fn)) is now asyncronous (i.e., it now
+ / really means $(setTimeout(fn)).
+ / https://jquery.com/upgrade-guide/3.0/#breaking-change-document-ready-handlers-are-now-asynchronous
+ /
+ / Since Shiny uses $() to schedule initShiny, shiny>=1.4 calls initShiny
+ / one tick later than it did before, which means staticRender() is
+ / called renderValue() earlier than (advanced) widget authors might be expecting.
+ / https://github.com/rstudio/shiny/issues/2630
+ /
+ / For a concrete example, leaflet has some methods (e.g., updateBounds)
+ / which reference Shiny methods registered in initShiny (e.g., setInputValue).
+ / Since leaflet is privy to this life-cycle, it knows to use setTimeout() to
+ / delay execution of those methods (until Shiny methods are ready)
+ / https://github.com/rstudio/leaflet/blob/18ec981/javascript/src/index.js#L266-L268
+ /
+ / Ideally widget authors wouldn't need to use this setTimeout() hack that
+ / leaflet uses to call Shiny methods on a staticRender(). In the long run,
+ / the logic initShiny should be broken up so that method registration happens
+ / right away, but binding happens later.
+ */
+ function maybeStaticRenderLater() {
+ if (shinyMode && has_jQuery3()) {
+ window.jQuery(window.HTMLWidgets.staticRender);
+ } else {
+ window.HTMLWidgets.staticRender();
+ }
+ }
+
+ if (document.addEventListener) {
+ document.addEventListener("DOMContentLoaded", function() {
+ document.removeEventListener("DOMContentLoaded", arguments.callee, false);
+ maybeStaticRenderLater();
+ }, false);
+ } else if (document.attachEvent) {
+ document.attachEvent("onreadystatechange", function() {
+ if (document.readyState === "complete") {
+ document.detachEvent("onreadystatechange", arguments.callee);
+ maybeStaticRenderLater();
+ }
+ });
+ }
+
+
+ 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] = tryEval(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/examples/output/aa/aa.candidates/results_revigo/BP_barplot.html b/examples/output/aa/aa.candidates/results_revigo/BP_barplot.html
new file mode 100644
index 0000000..76ffcec
--- /dev/null
+++ b/examples/output/aa/aa.candidates/results_revigo/BP_barplot.html
@@ -0,0 +1,14 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/examples/output/aa/aa.candidates/results_revigo/BP_barplot.png b/examples/output/aa/aa.candidates/results_revigo/BP_barplot.png
new file mode 100644
index 0000000..464b691
Binary files /dev/null and b/examples/output/aa/aa.candidates/results_revigo/BP_barplot.png differ
diff --git a/examples/output/aa/aa.candidates/results_revigo/CC_barplot.html b/examples/output/aa/aa.candidates/results_revigo/CC_barplot.html
new file mode 100644
index 0000000..5ea0737
--- /dev/null
+++ b/examples/output/aa/aa.candidates/results_revigo/CC_barplot.html
@@ -0,0 +1,14 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/examples/output/aa/aa.candidates/results_revigo/CC_barplot.png b/examples/output/aa/aa.candidates/results_revigo/CC_barplot.png
new file mode 100644
index 0000000..8bd0433
Binary files /dev/null and b/examples/output/aa/aa.candidates/results_revigo/CC_barplot.png differ
diff --git a/examples/output/aa/aa.candidates/results_revigo/MF_barplot.html b/examples/output/aa/aa.candidates/results_revigo/MF_barplot.html
new file mode 100644
index 0000000..acaddc1
--- /dev/null
+++ b/examples/output/aa/aa.candidates/results_revigo/MF_barplot.html
@@ -0,0 +1,14 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/examples/output/aa/aa.candidates/results_revigo/MF_barplot.png b/examples/output/aa/aa.candidates/results_revigo/MF_barplot.png
new file mode 100644
index 0000000..b389968
Binary files /dev/null and b/examples/output/aa/aa.candidates/results_revigo/MF_barplot.png differ
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_Rscript.R b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_Rscript.R
index 16a35c8..0c4195c 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_Rscript.R
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_Rscript.R
@@ -19,28 +19,28 @@ library(treemap) # treemap package by Martijn Tennekes
# Here is your data from Revigo. Scroll down for plot configuration options.
revigo.names <- c("term_ID","description","frequency","value","uniqueness","dispensability","representative");
-revigo.data <- rbind(c("GO:0002181","cytoplasmic translation",0.3974763229665376,22.2495144239621,0.580417500723756,0,"cytoplasmic translation"),
-c("GO:0000096","sulfur amino acid metabolic process",0.6045711859846593,2.2541128739161547,0.6232127385198889,0.53210148,"cytoplasmic translation"),
-c("GO:0000460","maturation of 5.8S rRNA",0.1803006726670273,3.2794866582215425,0.5961881148444329,0.65659493,"cytoplasmic translation"),
-c("GO:0000470","maturation of LSU-rRNA",0.20518715412917427,3.922886831195291,0.5921696185755898,0.59099573,"cytoplasmic translation"),
-c("GO:0002182","cytoplasmic translational elongation",0.009651922492400466,3.0268003580928236,0.6608289719738225,0.69099207,"cytoplasmic translation"),
-c("GO:0002183","cytoplasmic translational initiation",0.1243017760819051,3.5055139873691683,0.5989201892557875,0.48926856,"cytoplasmic translation"),
-c("GO:0006537","glutamate biosynthetic process",0.08242091117106017,2.1152806777703783,0.5769167337953903,0.67009017,"cytoplasmic translation"),
-c("GO:0009067","aspartate family amino acid biosynthetic process",0.7567688912721283,3.5055139873691683,0.49110425925572443,0.63775023,"cytoplasmic translation"),
-c("GO:0010467","gene expression",12.663260691525247,2.3263822734329542,0.5668346744466087,0.45657675,"cytoplasmic translation"),
-c("GO:0016053","organic acid biosynthetic process",4.4026914173902405,3.1869972932108914,0.498880589794459,0.21692113,"cytoplasmic translation"),
-c("GO:0016072","rRNA metabolic process",1.653535024007062,4.077529044837683,0.6509958545435159,0.21802309,"cytoplasmic translation"),
-c("GO:0042273","ribosomal large subunit biogenesis",0.3272829877619735,2.924208026340194,0.8914638945745725,0.63200998,"cytoplasmic translation"),
-c("GO:0043043","peptide biosynthetic process",4.592791896959665,13.773969815035858,0.5188172408277294,0.64900656,"cytoplasmic translation"),
-c("GO:0043603","amide metabolic process",6.707376287050344,11.747550569633349,0.7836221244810491,0.13247309,"cytoplasmic translation"),
-c("GO:0044237","cellular metabolic process",46.10331480933213,2.4174404971937933,0.8271563262130823,0.13458491,"cytoplasmic translation"),
-c("GO:0044271","cellular nitrogen compound biosynthetic process",12.957025677761646,4.182953402612982,0.5844507498260826,0.36321189,"cytoplasmic translation"),
-c("GO:1901564","organonitrogen compound metabolic process",27.31959408292786,3.2859366444593814,0.7142703174484127,0.27258733,"cytoplasmic translation"),
-c("GO:1901576","organic substance biosynthetic process",28.21764434528959,3.55381059144845,0.6043593845422406,0.53115188,"cytoplasmic translation"),
-c("GO:0006450","regulation of translational fidelity",0.29561600610151356,2.9163987279484807,1,-0,"regulation of translational fidelity"),
-c("GO:0006616","SRP-dependent cotranslational protein targeting to membrane, translocation",0.09292316902093718,2.2847539712701317,0.9855931345813477,0.008425,"SRP-dependent cotranslational protein targeting to membrane, translocation"),
-c("GO:0008152","metabolic process",57.597931274565454,2.4449763332997145,1,-0,"metabolic process"),
-c("GO:0098754","detoxification",0.9926322015147898,2.1668723485354233,1,-0,"detoxification"));
+revigo.data <- rbind(c("GO:0002181","cytoplasmic translation",0.30687006719783905,22.2495144239621,0.6537717495213964,0,"cytoplasmic translation"),
+c("GO:0000096","sulfur amino acid metabolic process",0.6402709259414305,2.2541128739161547,0.657305718971886,0.55631336,"cytoplasmic translation"),
+c("GO:0000460","maturation of 5.8S rRNA",0.13956353459239157,3.2794866582215425,0.6317435017052823,0.63698313,"cytoplasmic translation"),
+c("GO:0000470","maturation of LSU-rRNA",0.14326076431766677,3.922886831195291,0.6310538737514458,0.42351605,"cytoplasmic translation"),
+c("GO:0002183","cytoplasmic translational initiation",0.12346322869484458,3.5055139873691683,0.6531620701823336,0.46346812,"cytoplasmic translation"),
+c("GO:0006396","RNA processing",4.467702645863771,2.500143701854688,0.5765718660997399,0.62308399,"cytoplasmic translation"),
+c("GO:0006537","glutamate biosynthetic process",0.07835812805236687,2.1152806777703783,0.6004942068949972,0.50919689,"cytoplasmic translation"),
+c("GO:0008652","amino acid biosynthetic process",2.828030852968805,2.3819145278208653,0.6436108455427967,0.26113292,"cytoplasmic translation"),
+c("GO:0009067","aspartate family amino acid biosynthetic process",0.7271117442502224,3.5055139873691683,0.5174576447828639,0.64402474,"cytoplasmic translation"),
+c("GO:0010467","gene expression",13.109073483873399,2.3263822734329542,0.5894919899029382,0.42780084,"cytoplasmic translation"),
+c("GO:0016053","organic acid biosynthetic process",4.319149498310446,3.1869972932108914,0.5370530185553284,0.24790322,"cytoplasmic translation"),
+c("GO:0016072","rRNA metabolic process",1.511795030653258,4.077529044837683,0.7579162328297245,0.16660899,"cytoplasmic translation"),
+c("GO:0042273","ribosomal large subunit biogenesis",0.4347743795865312,2.924208026340194,0.8833192327249768,0.62751481,"cytoplasmic translation"),
+c("GO:0043043","peptide biosynthetic process",0.21889418283329953,13.773969815035858,0.8118289533880934,0.14705947,"cytoplasmic translation"),
+c("GO:0006450","regulation of translational fidelity",0.2893564387600043,2.9163987279484807,1,-0,"regulation of translational fidelity"),
+c("GO:0006616","SRP-dependent cotranslational protein targeting to membrane, translocation",0.03596947190252802,2.2847539712701317,0.9821667871820254,0.0127822,"SRP-dependent cotranslational protein targeting to membrane, translocation"),
+c("GO:0008152","metabolic process",55.714893667314946,2.4449763332997145,1,-0,"metabolic process"),
+c("GO:0009058","biosynthetic process",29.083973867363177,4.182953402612982,0.8421260604475806,0.09568932,"biosynthetic process"),
+c("GO:0044237","cellular metabolic process",35.76590662147671,2.4174404971937933,0.832448903671638,0.22891344,"biosynthetic process"),
+c("GO:1901564","organonitrogen compound metabolic process",27.244450553230372,3.2859366444593814,0.8440728793195891,0.20434134,"biosynthetic process"),
+c("GO:0043603","amide metabolic process",1.5312702295563652,11.747550569633349,0.9003064304677143,0.05198569,"amide metabolic process"),
+c("GO:0098754","detoxification",1.0329101107303773,2.1668723485354233,1,-0,"detoxification"));
stuff <- data.frame(revigo.data);
names(stuff) <- revigo.names;
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_TreeMap.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_TreeMap.tsv
index 12d6544..21533cb 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_TreeMap.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_TreeMap.tsv
@@ -3,25 +3,25 @@
# threshold to detect redundancies (c=0.10) and fill the 'representative' column, while normally c>=0.4 is recommended.
# To export a reduced-redundancy set of GO terms, go to the Scatterplot or Table tab, and export from there.
TermID Name Frequency Value Uniqueness Dispensability Representative
-"GO:0002181" "cytoplasmic translation" 0.3974763229665376 -22.2495144239621 0.580417500723756 0 null
-"GO:0000096" "sulfur amino acid metabolic process" 0.6045711859846593 -2.2541128739161547 0.6232127385198889 0.53210148 "cytoplasmic translation"
-"GO:0000460" "maturation of 5.8S rRNA" 0.1803006726670273 -3.2794866582215425 0.5961881148444329 0.65659493 "cytoplasmic translation"
-"GO:0000470" "maturation of LSU-rRNA" 0.20518715412917427 -3.922886831195291 0.5921696185755898 0.59099573 "cytoplasmic translation"
-"GO:0002182" "cytoplasmic translational elongation" 0.009651922492400466 -3.0268003580928236 0.6608289719738225 0.69099207 "cytoplasmic translation"
-"GO:0002183" "cytoplasmic translational initiation" 0.1243017760819051 -3.5055139873691683 0.5989201892557875 0.48926856 "cytoplasmic translation"
-"GO:0006537" "glutamate biosynthetic process" 0.08242091117106017 -2.1152806777703783 0.5769167337953903 0.67009017 "cytoplasmic translation"
-"GO:0009067" "aspartate family amino acid biosynthetic process" 0.7567688912721283 -3.5055139873691683 0.49110425925572443 0.63775023 "cytoplasmic translation"
-"GO:0010467" "gene expression" 12.663260691525247 -2.3263822734329542 0.5668346744466087 0.45657675 "cytoplasmic translation"
-"GO:0016053" "organic acid biosynthetic process" 4.4026914173902405 -3.1869972932108914 0.498880589794459 0.21692113 "cytoplasmic translation"
-"GO:0016072" "rRNA metabolic process" 1.653535024007062 -4.077529044837683 0.6509958545435159 0.21802309 "cytoplasmic translation"
-"GO:0042273" "ribosomal large subunit biogenesis" 0.3272829877619735 -2.924208026340194 0.8914638945745725 0.63200998 "cytoplasmic translation"
-"GO:0043043" "peptide biosynthetic process" 4.592791896959665 -13.773969815035858 0.5188172408277294 0.64900656 "cytoplasmic translation"
-"GO:0043603" "amide metabolic process" 6.707376287050344 -11.747550569633349 0.7836221244810491 0.13247309 "cytoplasmic translation"
-"GO:0044237" "cellular metabolic process" 46.10331480933213 -2.4174404971937933 0.8271563262130823 0.13458491 "cytoplasmic translation"
-"GO:0044271" "cellular nitrogen compound biosynthetic process" 12.957025677761646 -4.182953402612982 0.5844507498260826 0.36321189 "cytoplasmic translation"
-"GO:1901564" "organonitrogen compound metabolic process" 27.31959408292786 -3.2859366444593814 0.7142703174484127 0.27258733 "cytoplasmic translation"
-"GO:1901576" "organic substance biosynthetic process" 28.21764434528959 -3.55381059144845 0.6043593845422406 0.53115188 "cytoplasmic translation"
-"GO:0006450" "regulation of translational fidelity" 0.29561600610151356 -2.9163987279484807 1 -0 null
-"GO:0006616" "SRP-dependent cotranslational protein targeting to membrane, translocation" 0.09292316902093718 -2.2847539712701317 0.9855931345813477 0.008425 null
-"GO:0008152" "metabolic process" 57.597931274565454 -2.4449763332997145 1 -0 null
-"GO:0098754" "detoxification" 0.9926322015147898 -2.1668723485354233 1 -0 null
+"GO:0002181" "cytoplasmic translation" 0.30687006719783905 -22.2495144239621 0.6537717495213964 0 null
+"GO:0000096" "sulfur amino acid metabolic process" 0.6402709259414305 -2.2541128739161547 0.657305718971886 0.55631336 "cytoplasmic translation"
+"GO:0000460" "maturation of 5.8S rRNA" 0.13956353459239157 -3.2794866582215425 0.6317435017052823 0.63698313 "cytoplasmic translation"
+"GO:0000470" "maturation of LSU-rRNA" 0.14326076431766677 -3.922886831195291 0.6310538737514458 0.42351605 "cytoplasmic translation"
+"GO:0002183" "cytoplasmic translational initiation" 0.12346322869484458 -3.5055139873691683 0.6531620701823336 0.46346812 "cytoplasmic translation"
+"GO:0006396" "RNA processing" 4.467702645863771 -2.500143701854688 0.5765718660997399 0.62308399 "cytoplasmic translation"
+"GO:0006537" "glutamate biosynthetic process" 0.07835812805236687 -2.1152806777703783 0.6004942068949972 0.50919689 "cytoplasmic translation"
+"GO:0008652" "amino acid biosynthetic process" 2.828030852968805 -2.3819145278208653 0.6436108455427967 0.26113292 "cytoplasmic translation"
+"GO:0009067" "aspartate family amino acid biosynthetic process" 0.7271117442502224 -3.5055139873691683 0.5174576447828639 0.64402474 "cytoplasmic translation"
+"GO:0010467" "gene expression" 13.109073483873399 -2.3263822734329542 0.5894919899029382 0.42780084 "cytoplasmic translation"
+"GO:0016053" "organic acid biosynthetic process" 4.319149498310446 -3.1869972932108914 0.5370530185553284 0.24790322 "cytoplasmic translation"
+"GO:0016072" "rRNA metabolic process" 1.511795030653258 -4.077529044837683 0.7579162328297245 0.16660899 "cytoplasmic translation"
+"GO:0042273" "ribosomal large subunit biogenesis" 0.4347743795865312 -2.924208026340194 0.8833192327249768 0.62751481 "cytoplasmic translation"
+"GO:0043043" "peptide biosynthetic process" 0.21889418283329953 -13.773969815035858 0.8118289533880934 0.14705947 "cytoplasmic translation"
+"GO:0006450" "regulation of translational fidelity" 0.2893564387600043 -2.9163987279484807 1 -0 null
+"GO:0006616" "SRP-dependent cotranslational protein targeting to membrane, translocation" 0.03596947190252802 -2.2847539712701317 0.9821667871820254 0.0127822 null
+"GO:0008152" "metabolic process" 55.714893667314946 -2.4449763332997145 1 -0 null
+"GO:0009058" "biosynthetic process" 29.083973867363177 -4.182953402612982 0.8421260604475806 0.09568932 null
+"GO:0044237" "cellular metabolic process" 35.76590662147671 -2.4174404971937933 0.832448903671638 0.22891344 "biosynthetic process"
+"GO:1901564" "organonitrogen compound metabolic process" 27.244450553230372 -3.2859366444593814 0.8440728793195891 0.20434134 "biosynthetic process"
+"GO:0043603" "amide metabolic process" 1.5312702295563652 -11.747550569633349 0.9003064304677143 0.05198569 null
+"GO:0098754" "detoxification" 1.0329101107303773 -2.1668723485354233 1 -0 null
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_barplot.png b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_barplot.png
deleted file mode 100644
index 4e0ef49..0000000
Binary files a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_barplot.png and /dev/null differ
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_scatterPlot.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_scatterPlot.tsv
index 53d62c3..ae12cc4 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_scatterPlot.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_scatterPlot.tsv
@@ -1,28 +1,27 @@
TermID Name Value LogSize Frequency Uniqueness Dispensability PC_0 PC_1 Representative
-"GO:0000096" "sulfur amino acid metabolic process" -2.2541128739161547 5.389678072680837 0.6045711859846593 0.6232127385198889 0.53210148 -8.19211152476106 4.1623549068591235 null
-"GO:0000460" "maturation of 5.8S rRNA" -3.2794866582215425 4.86423214121635 0.1803006726670273 0.5961881148444329 0.65659493 -4.90930068668122 -3.7251215405386042 null
-"GO:0000470" "maturation of LSU-rRNA" -3.922886831195291 4.920384242178358 0.20518715412917427 0.5921696185755898 0.59099573 -4.660303724632927 -3.486745807453323 null
-"GO:0002181" "cytoplasmic translation" -22.2495144239621 5.207542813955311 0.3974763229665376 0.580417500723756 0 -6.733070629623954 -1.0469559621547224 null
-"GO:0002182" "cytoplasmic translational elongation" -3.0268003580928236 3.592953571547866 0.009651922492400466 0.6608289719738225 0.69099207 -7.974447303836637 -2.6298293591098107 null
-"GO:0002183" "cytoplasmic translational initiation" -3.5055139873691683 4.702714802874462 0.1243017760819051 0.5989201892557875 0.48926856 -7.309676091978607 -1.6957067950436102 null
-"GO:0006450" "regulation of translational fidelity" -2.9163987279484807 5.078960423555517 0.29561600610151356 1 -0 1.8743535879509483 -6.014867870437558 null
-"GO:0006537" "glutamate biosynthetic process" -2.1152806777703783 4.524279255847971 0.08242091117106017 0.5769167337953903 0.67009017 -8.645134358996884 1.5071227009122943 null
-"GO:0006616" "SRP-dependent cotranslational protein targeting to membrane, translocation" -2.2847539712701317 4.576364389089749 0.09292316902093718 0.9855931345813477 0.008425 3.641118976980864 -2.8198694344781536 null
-"GO:0008152" "metabolic process" -2.4449763332997145 7.368635761264388 57.597931274565454 1 -0 3.351229284817593 3.88642029790243 null
-"GO:0009067" "aspartate family amino acid biosynthetic process" -3.5055139873691683 5.4871935429333805 0.7567688912721283 0.49110425925572443 0.63775023 -7.5622855293190465 1.3980260368963608 null
-"GO:0071265" "L-methionine biosynthetic process" -2.1152806777703783 4.696723243167566 0.12259864062678538 0.5455706229468514 0.79000223 null null 9067
-"GO:0010467" "gene expression" -2.3263822734329542 6.710774489460372 12.663260691525247 0.5668346744466087 0.45657675 -5.1238813681355655 -0.8776831393683537 null
-"GO:0016053" "organic acid biosynthetic process" -3.1869972932108914 6.25194734754039 4.4026914173902405 0.498880589794459 0.21692113 -7.167457420308251 1.975319292155832 null
-"GO:0008652" "amino acid biosynthetic process" -2.3819145278208653 6.036271093732633 2.679426429329935 0.456227173770196 0.81183982 null null 16053
-"GO:0019752" "carboxylic acid metabolic process" -2.6070633639376193 6.545215051125638 8.649401753337283 0.5782522159557706 0.7862514 null null 16053
-"GO:1901607" "alpha-amino acid biosynthetic process" -2.7748224993526356 5.980129321456284 2.354507127387729 0.45913717446622804 0.7430888 null null 16053
-"GO:0016072" "rRNA metabolic process" -4.077529044837683 5.826642903003747 1.653535024007062 0.6509958545435159 0.21802309 -3.1846561551110635 -2.7837013109051734 null
-"GO:0034470" "ncRNA processing" -2.500143701854688 6.093096192594597 3.0539855982274378 0.5395203640344499 0.80122612 null null 16072
-"GO:0042273" "ribosomal large subunit biogenesis" -2.924208026340194 5.12315555918394 0.3272829877619735 0.8914638945745725 0.63200998 -3.176832048288636 -7.68135039131261 null
-"GO:0043043" "peptide biosynthetic process" -13.773969815035858 6.2703058580872275 4.592791896959665 0.5188172408277294 0.64900656 -6.180021712236918 0.2515890574004989 null
-"GO:0043603" "amide metabolic process" -11.747550569633349 6.434781688128081 6.707376287050344 0.7836221244810491 0.13247309 -3.0527005554870885 5.931447772718988 null
-"GO:0044237" "cellular metabolic process" -2.4174404971937933 7.271961032709232 46.10331480933213 0.8271563262130823 0.13458491 -0.3840526310011623 5.575821737199759 null
-"GO:0044271" "cellular nitrogen compound biosynthetic process" -4.182953402612982 6.72073425943514 12.957025677761646 0.5844507498260826 0.36321189 -4.45766880068408 0.8204745927748489 null
-"GO:0098754" "detoxification" -2.1668723485354233 5.605018295584764 0.9926322015147898 1 -0 4.0770704785548775 0.4444744373666363 null
-"GO:1901564" "organonitrogen compound metabolic process" -3.2859366444593814 7.044703138835916 27.31959408292786 0.7142703174484127 0.27258733 -3.0017902643294314 3.4877746923003006 null
-"GO:1901576" "organic substance biosynthetic process" -3.55381059144845 7.058749650643281 28.21764434528959 0.6043593845422406 0.53115188 -4.48341486625932 1.2711997230213565 null
+"GO:0000096" "sulfur amino acid metabolic process" -2.2541128739161547 5.366241729893149 0.6402709259414305 0.657305718971886 0.55631336 7.670218377436888 5.074734497931802 null
+"GO:0000460" "maturation of 5.8S rRNA" -3.2794866582215425 4.70465661264031 0.13956353459239157 0.6317435017052823 0.63698313 6.029202349407482 -2.0957531009299464 null
+"GO:0000470" "maturation of LSU-rRNA" -3.922886831195291 4.716011695371454 0.14326076431766677 0.6310538737514458 0.42351605 5.695942591948317 -2.1309395318748834 null
+"GO:0002181" "cytoplasmic translation" -22.2495144239621 5.0468345071957454 0.30687006719783905 0.6537717495213964 0 7.097160067771662 0.5130176435478488 null
+"GO:0002183" "cytoplasmic translational initiation" -3.5055139873691683 4.651423400759052 0.12346322869484458 0.6531620701823336 0.46346812 7.709652587044969 0.41248684489695797 null
+"GO:0002182" "cytoplasmic translational elongation" -3.0268003580928236 3.611510887126656 0.011259745072428924 0.7008982635052964 0.7307446 null null 2183
+"GO:0006396" "RNA processing" -2.500143701854688 6.209960607922796 4.467702645863771 0.5765718660997399 0.62308399 5.723677528788202 0.11048640642531295 null
+"GO:0006450" "regulation of translational fidelity" -2.9163987279484807 5.021313365484695 0.2893564387600043 1 -0 -4.28539285659919 3.1707916812973607 null
+"GO:0006537" "glutamate biosynthetic process" -2.1152806777703783 4.453975401295882 0.07835812805236687 0.6004942068949972 0.50919689 6.869458826118269 3.5683406334447563 null
+"GO:0006616" "SRP-dependent cotranslational protein targeting to membrane, translocation" -2.2847539712701317 4.115843404112816 0.03596947190252802 0.9821667871820254 0.0127822 -0.05614455429915128 -6.472311212489294 null
+"GO:0008152" "metabolic process" -2.4449763332997145 7.305847407252974 55.714893667314946 1 -0 -3.8201874278990613 -2.247907574024415 null
+"GO:0008652" "amino acid biosynthetic process" -2.3819145278208653 6.011360646034466 2.828030852968805 0.6436108455427967 0.26113292 4.324099157961267 2.8817297417135315 null
+"GO:0009058" "biosynthetic process" -4.182953402612982 7.023529866667043 29.083973867363177 0.8421260604475806 0.09568932 -0.32782146419002084 6.941951069975038 null
+"GO:0009067" "aspartate family amino acid biosynthetic process" -3.5055139873691683 5.421478884701441 0.7271117442502224 0.5174576447828639 0.64402474 6.630268723764757 2.8766634643838804 null
+"GO:0071265" "L-methionine biosynthetic process" -2.1152806777703783 4.653829738227294 0.12414922735475033 0.5625616289400958 0.80622585 null null 9067
+"GO:1901607" "alpha-amino acid biosynthetic process" -2.7748224993526356 5.967672911508309 2.557386474040447 0.4787719659504659 0.80669187 null null 9067
+"GO:0010467" "gene expression" -2.3263822734329542 6.677448168991759 13.109073483873399 0.5894919899029382 0.42780084 4.964493966344422 1.3698940504890067 null
+"GO:0016053" "organic acid biosynthetic process" -3.1869972932108914 6.195274593300221 4.319149498310446 0.5370530185553284 0.24790322 5.8222837532146405 3.171578106402449 null
+"GO:0019752" "carboxylic acid metabolic process" -2.6070633639376193 6.461861837538785 7.979682427802705 0.5939340667022646 0.80381806 null null 16053
+"GO:0016072" "rRNA metabolic process" -4.077529044837683 5.739369784674073 1.511795030653258 0.7579162328297245 0.16660899 6.918518836035723 -3.795088680646227 null
+"GO:0042273" "ribosomal large subunit biogenesis" -2.924208026340194 5.198142775779092 0.4347743795865312 0.8833192327249768 0.62751481 4.046098457855668 -6.186618540947003 null
+"GO:0043043" "peptide biosynthetic process" -13.773969815035858 4.900115766039295 0.21889418283329953 0.8118289533880934 0.14705947 1.5022722002138995 0.3378994031435677 null
+"GO:0043603" "amide metabolic process" -11.747550569633349 5.744928700343905 1.5312702295563652 0.9003064304677143 0.05198569 -4.446125246778525 0.3856374872791094 null
+"GO:0044237" "cellular metabolic process" -2.4174404971937933 7.11334535158082 35.76590662147671 0.832448903671638 0.22891344 0.803832834909572 7.407497045499689 null
+"GO:0098754" "detoxification" -2.1668723485354233 5.57393976671842 1.0329101107303773 1 -0 -2.3347551203061094 -4.562703588467398 null
+"GO:1901564" "organonitrogen compound metabolic process" -3.2859366444593814 6.99515417748169 27.244450553230372 0.8440728793195891 0.20434134 -1.3079240977971356 5.9936037821457475 null
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_table.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_table.tsv
index 2b8fcfe..9a3a7d0 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_table.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_table.tsv
@@ -1,28 +1,27 @@
TermID Name Value LogSize Frequency Uniqueness Dispensability Representative
-"GO:0000096" "sulfur amino acid metabolic process" -2.2541128739161547 5.389678072680837 0.6045711859846593 0.6232127385198889 0.53210148 null
-"GO:0000460" "maturation of 5.8S rRNA" -3.2794866582215425 4.86423214121635 0.1803006726670273 0.5961881148444329 0.65659493 null
-"GO:0000470" "maturation of LSU-rRNA" -3.922886831195291 4.920384242178358 0.20518715412917427 0.5921696185755898 0.59099573 null
-"GO:0002181" "cytoplasmic translation" -22.2495144239621 5.207542813955311 0.3974763229665376 0.580417500723756 0 null
-"GO:0002182" "cytoplasmic translational elongation" -3.0268003580928236 3.592953571547866 0.009651922492400466 0.6608289719738225 0.69099207 null
-"GO:0002183" "cytoplasmic translational initiation" -3.5055139873691683 4.702714802874462 0.1243017760819051 0.5989201892557875 0.48926856 null
-"GO:0006450" "regulation of translational fidelity" -2.9163987279484807 5.078960423555517 0.29561600610151356 1 -0 null
-"GO:0006537" "glutamate biosynthetic process" -2.1152806777703783 4.524279255847971 0.08242091117106017 0.5769167337953903 0.67009017 null
-"GO:0006616" "SRP-dependent cotranslational protein targeting to membrane, translocation" -2.2847539712701317 4.576364389089749 0.09292316902093718 0.9855931345813477 0.008425 null
-"GO:0008152" "metabolic process" -2.4449763332997145 7.368635761264388 57.597931274565454 1 -0 null
-"GO:0009067" "aspartate family amino acid biosynthetic process" -3.5055139873691683 5.4871935429333805 0.7567688912721283 0.49110425925572443 0.63775023 null
-"GO:0071265" "L-methionine biosynthetic process" -2.1152806777703783 4.696723243167566 0.12259864062678538 0.5455706229468514 0.79000223 9067
-"GO:0010467" "gene expression" -2.3263822734329542 6.710774489460372 12.663260691525247 0.5668346744466087 0.45657675 null
-"GO:0016053" "organic acid biosynthetic process" -3.1869972932108914 6.25194734754039 4.4026914173902405 0.498880589794459 0.21692113 null
-"GO:0008652" "amino acid biosynthetic process" -2.3819145278208653 6.036271093732633 2.679426429329935 0.456227173770196 0.81183982 16053
-"GO:0019752" "carboxylic acid metabolic process" -2.6070633639376193 6.545215051125638 8.649401753337283 0.5782522159557706 0.7862514 16053
-"GO:1901607" "alpha-amino acid biosynthetic process" -2.7748224993526356 5.980129321456284 2.354507127387729 0.45913717446622804 0.7430888 16053
-"GO:0016072" "rRNA metabolic process" -4.077529044837683 5.826642903003747 1.653535024007062 0.6509958545435159 0.21802309 null
-"GO:0034470" "ncRNA processing" -2.500143701854688 6.093096192594597 3.0539855982274378 0.5395203640344499 0.80122612 16072
-"GO:0042273" "ribosomal large subunit biogenesis" -2.924208026340194 5.12315555918394 0.3272829877619735 0.8914638945745725 0.63200998 null
-"GO:0043043" "peptide biosynthetic process" -13.773969815035858 6.2703058580872275 4.592791896959665 0.5188172408277294 0.64900656 null
-"GO:0043603" "amide metabolic process" -11.747550569633349 6.434781688128081 6.707376287050344 0.7836221244810491 0.13247309 null
-"GO:0044237" "cellular metabolic process" -2.4174404971937933 7.271961032709232 46.10331480933213 0.8271563262130823 0.13458491 null
-"GO:0044271" "cellular nitrogen compound biosynthetic process" -4.182953402612982 6.72073425943514 12.957025677761646 0.5844507498260826 0.36321189 null
-"GO:0098754" "detoxification" -2.1668723485354233 5.605018295584764 0.9926322015147898 1 -0 null
-"GO:1901564" "organonitrogen compound metabolic process" -3.2859366444593814 7.044703138835916 27.31959408292786 0.7142703174484127 0.27258733 null
-"GO:1901576" "organic substance biosynthetic process" -3.55381059144845 7.058749650643281 28.21764434528959 0.6043593845422406 0.53115188 null
+"GO:0000096" "sulfur amino acid metabolic process" -2.2541128739161547 5.366241729893149 0.6402709259414305 0.657305718971886 0.55631336 null
+"GO:0000460" "maturation of 5.8S rRNA" -3.2794866582215425 4.70465661264031 0.13956353459239157 0.6317435017052823 0.63698313 null
+"GO:0000470" "maturation of LSU-rRNA" -3.922886831195291 4.716011695371454 0.14326076431766677 0.6310538737514458 0.42351605 null
+"GO:0002181" "cytoplasmic translation" -22.2495144239621 5.0468345071957454 0.30687006719783905 0.6537717495213964 0 null
+"GO:0002183" "cytoplasmic translational initiation" -3.5055139873691683 4.651423400759052 0.12346322869484458 0.6531620701823336 0.46346812 null
+"GO:0002182" "cytoplasmic translational elongation" -3.0268003580928236 3.611510887126656 0.011259745072428924 0.7008982635052964 0.7307446 2183
+"GO:0006396" "RNA processing" -2.500143701854688 6.209960607922796 4.467702645863771 0.5765718660997399 0.62308399 null
+"GO:0006450" "regulation of translational fidelity" -2.9163987279484807 5.021313365484695 0.2893564387600043 1 -0 null
+"GO:0006537" "glutamate biosynthetic process" -2.1152806777703783 4.453975401295882 0.07835812805236687 0.6004942068949972 0.50919689 null
+"GO:0006616" "SRP-dependent cotranslational protein targeting to membrane, translocation" -2.2847539712701317 4.115843404112816 0.03596947190252802 0.9821667871820254 0.0127822 null
+"GO:0008152" "metabolic process" -2.4449763332997145 7.305847407252974 55.714893667314946 1 -0 null
+"GO:0008652" "amino acid biosynthetic process" -2.3819145278208653 6.011360646034466 2.828030852968805 0.6436108455427967 0.26113292 null
+"GO:0009058" "biosynthetic process" -4.182953402612982 7.023529866667043 29.083973867363177 0.8421260604475806 0.09568932 null
+"GO:0009067" "aspartate family amino acid biosynthetic process" -3.5055139873691683 5.421478884701441 0.7271117442502224 0.5174576447828639 0.64402474 null
+"GO:0071265" "L-methionine biosynthetic process" -2.1152806777703783 4.653829738227294 0.12414922735475033 0.5625616289400958 0.80622585 9067
+"GO:1901607" "alpha-amino acid biosynthetic process" -2.7748224993526356 5.967672911508309 2.557386474040447 0.4787719659504659 0.80669187 9067
+"GO:0010467" "gene expression" -2.3263822734329542 6.677448168991759 13.109073483873399 0.5894919899029382 0.42780084 null
+"GO:0016053" "organic acid biosynthetic process" -3.1869972932108914 6.195274593300221 4.319149498310446 0.5370530185553284 0.24790322 null
+"GO:0019752" "carboxylic acid metabolic process" -2.6070633639376193 6.461861837538785 7.979682427802705 0.5939340667022646 0.80381806 16053
+"GO:0016072" "rRNA metabolic process" -4.077529044837683 5.739369784674073 1.511795030653258 0.7579162328297245 0.16660899 null
+"GO:0042273" "ribosomal large subunit biogenesis" -2.924208026340194 5.198142775779092 0.4347743795865312 0.8833192327249768 0.62751481 null
+"GO:0043043" "peptide biosynthetic process" -13.773969815035858 4.900115766039295 0.21889418283329953 0.8118289533880934 0.14705947 null
+"GO:0043603" "amide metabolic process" -11.747550569633349 5.744928700343905 1.5312702295563652 0.9003064304677143 0.05198569 null
+"GO:0044237" "cellular metabolic process" -2.4174404971937933 7.11334535158082 35.76590662147671 0.832448903671638 0.22891344 null
+"GO:0098754" "detoxification" -2.1668723485354233 5.57393976671842 1.0329101107303773 1 -0 null
+"GO:1901564" "organonitrogen compound metabolic process" -3.2859366444593814 6.99515417748169 27.244450553230372 0.8440728793195891 0.20434134 null
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_treemap.pdf b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_treemap.pdf
index bd72639..5987806 100644
Binary files a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_treemap.pdf and b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_BP_treemap.pdf differ
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_Rscript.R b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_Rscript.R
index 81c3a23..c1329c0 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_Rscript.R
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_Rscript.R
@@ -19,12 +19,12 @@ library(treemap) # treemap package by Martijn Tennekes
# Here is your data from Revigo. Scroll down for plot configuration options.
revigo.names <- c("term_ID","description","frequency","value","uniqueness","dispensability","representative");
-revigo.data <- rbind(c("GO:0005737","cytoplasm",43.076660800468886,2.421761796101055,0.8888902750046057,0.08859538,"cytoplasm"),
-c("GO:0022625","cytosolic large ribosomal subunit",1.014469728138433,12.113076227493746,0.33018935796424503,0,"cytosolic large ribosomal subunit"),
-c("GO:0000322","storage vacuole",0.2661182824452727,3.996407586417781,0.8555104067946925,0.12655094,"cytosolic large ribosomal subunit"),
-c("GO:0005852","eukaryotic translation initiation factor 3 complex",0.08561256229366826,2.840897860731786,0.6744908630409379,0.22333355,"cytosolic large ribosomal subunit"),
-c("GO:0030687","preribosome, large subunit precursor",0.1323907395608457,4.0721192326205085,0.4963716015302116,0.53614612,"cytosolic large ribosomal subunit"),
-c("GO:1990904","ribonucleoprotein complex",4.315842197772249,3.3638802864553807,0.6093677891596602,0.33654169,"cytosolic large ribosomal subunit"));
+revigo.data <- rbind(c("GO:0022625","cytosolic large ribosomal subunit",0.6422496099261846,12.113076227493746,0.34085524602774525,0,"cytosolic large ribosomal subunit"),
+c("GO:0000322","storage vacuole",0.1778201926099983,3.996407586417781,0.8428127851699823,0.12770953,"cytosolic large ribosomal subunit"),
+c("GO:0005737","cytoplasm",36.38509412593251,2.421761796101055,0.8619152465722402,0.10701902,"cytosolic large ribosomal subunit"),
+c("GO:0005852","eukaryotic translation initiation factor 3 complex",0.09985555503264143,2.840897860731786,0.6456414810665522,0.23478132,"cytosolic large ribosomal subunit"),
+c("GO:0030687","preribosome, large subunit precursor",0.10178817133005495,4.0721192326205085,0.5094292084898253,0.50042336,"cytosolic large ribosomal subunit"),
+c("GO:1990904","ribonucleoprotein complex",4.396406893146647,3.3638802864553807,0.592507283898729,0.34351463,"cytosolic large ribosomal subunit"));
stuff <- data.frame(revigo.data);
names(stuff) <- revigo.names;
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_TreeMap.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_TreeMap.tsv
index 85b747f..a3de7e3 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_TreeMap.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_TreeMap.tsv
@@ -3,9 +3,9 @@
# threshold to detect redundancies (c=0.10) and fill the 'representative' column, while normally c>=0.4 is recommended.
# To export a reduced-redundancy set of GO terms, go to the Scatterplot or Table tab, and export from there.
TermID Name Frequency Value Uniqueness Dispensability Representative
-"GO:0005737" "cytoplasm" 43.076660800468886 -2.421761796101055 0.8888902750046057 0.08859538 null
-"GO:0022625" "cytosolic large ribosomal subunit" 1.014469728138433 -12.113076227493746 0.33018935796424503 0 null
-"GO:0000322" "storage vacuole" 0.2661182824452727 -3.996407586417781 0.8555104067946925 0.12655094 "cytosolic large ribosomal subunit"
-"GO:0005852" "eukaryotic translation initiation factor 3 complex" 0.08561256229366826 -2.840897860731786 0.6744908630409379 0.22333355 "cytosolic large ribosomal subunit"
-"GO:0030687" "preribosome, large subunit precursor" 0.1323907395608457 -4.0721192326205085 0.4963716015302116 0.53614612 "cytosolic large ribosomal subunit"
-"GO:1990904" "ribonucleoprotein complex" 4.315842197772249 -3.3638802864553807 0.6093677891596602 0.33654169 "cytosolic large ribosomal subunit"
+"GO:0022625" "cytosolic large ribosomal subunit" 0.6422496099261846 -12.113076227493746 0.34085524602774525 0 null
+"GO:0000322" "storage vacuole" 0.1778201926099983 -3.996407586417781 0.8428127851699823 0.12770953 "cytosolic large ribosomal subunit"
+"GO:0005737" "cytoplasm" 36.38509412593251 -2.421761796101055 0.8619152465722402 0.10701902 "cytosolic large ribosomal subunit"
+"GO:0005852" "eukaryotic translation initiation factor 3 complex" 0.09985555503264143 -2.840897860731786 0.6456414810665522 0.23478132 "cytosolic large ribosomal subunit"
+"GO:0030687" "preribosome, large subunit precursor" 0.10178817133005495 -4.0721192326205085 0.5094292084898253 0.50042336 "cytosolic large ribosomal subunit"
+"GO:1990904" "ribonucleoprotein complex" 4.396406893146647 -3.3638802864553807 0.592507283898729 0.34351463 "cytosolic large ribosomal subunit"
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_barplot.png b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_barplot.png
deleted file mode 100644
index 361f11b..0000000
Binary files a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_barplot.png and /dev/null differ
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_scatterPlot.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_scatterPlot.tsv
index 854bfca..96e2598 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_scatterPlot.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_scatterPlot.tsv
@@ -1,9 +1,9 @@
TermID Name Value LogSize Frequency Uniqueness Dispensability PC_0 PC_1 Representative
-"GO:0000322" "storage vacuole" -3.996407586417781 5.029793525850104 0.2661182824452727 0.8555104067946925 0.12655094 -2.6937657983416528 -5.284306621376451 null
-"GO:0005737" "cytoplasm" -2.421761796101055 7.238956814544198 43.076660800468886 0.8888902750046057 0.08859538 -4.093237438046929 4.002248887489144 null
-"GO:0005852" "eukaryotic translation initiation factor 3 complex" -2.840897860731786 4.537264858754543 0.08561256229366826 0.6744908630409379 0.22333355 4.558358641611579 3.1384207096374523 null
-"GO:0022625" "cytosolic large ribosomal subunit" -12.113076227493746 5.610954914935405 1.014469728138433 0.33018935796424503 0 4.031428075465963 -1.4212980375697013 null
-"GO:0022627" "cytosolic small ribosomal subunit" -2.3628115636350517 5.314539224168974 0.5126516507707168 0.35523486736625104 0.83441369 null null 22625
-"GO:0044391" "ribosomal subunit" -6.05324848933085 5.901851569419728 1.9821488551869784 0.32421904182325845 0.83207123 null null 22625
-"GO:0030687" "preribosome, large subunit precursor" -4.0721192326205085 4.726580518201694 0.1323907395608457 0.4963716015302116 0.53614612 5.560654203177438 -1.9944861339979993 null
-"GO:1990904" "ribonucleoprotein complex" -3.3638802864553807 6.239780566048521 4.315842197772249 0.6093677891596602 0.33654169 5.823022438146492 0.7202723484791583 null
+"GO:0000322" "storage vacuole" -3.996407586417781 4.805201710439948 0.1778201926099983 0.8428127851699823 0.12770953 -2.966747229135958 5.1110746607049204 null
+"GO:0005737" "cytoplasm" -2.421761796101055 7.116137368897206 36.38509412593251 0.8619152465722402 0.10701902 -3.748567266781315 -4.296822822574382 null
+"GO:0005852" "eukaryotic translation initiation factor 3 complex" -2.840897860731786 4.5545981742240045 0.09985555503264143 0.6456414810665522 0.23478132 4.903227171118142 -2.76240350772735 null
+"GO:0022625" "cytosolic large ribosomal subunit" -12.113076227493746 5.3629195651410235 0.6422496099261846 0.34085524602774525 0 3.6723275469377645 1.2996018798019329 null
+"GO:0022627" "cytosolic small ribosomal subunit" -2.3628115636350517 5.098875518374249 0.3496698818458546 0.3615708066454031 0.84980024 null null 22625
+"GO:0044391" "ribosomal subunit" -6.05324848933085 5.773268492313049 1.6521669390616007 0.3420516961913126 0.74995524 null null 22625
+"GO:0030687" "preribosome, large subunit precursor" -4.0721192326205085 4.562923026436936 0.10178817133005495 0.5094292084898253 0.50042336 5.400057329861363 2.1045520996152285 null
+"GO:1990904" "ribonucleoprotein complex" -3.3638802864553807 6.19831198812342 4.396406893146647 0.592507283898729 0.34351463 5.850993909444077 -0.4258635492138028 null
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_table.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_table.tsv
index 6ed7547..de30e55 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_table.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_table.tsv
@@ -1,9 +1,9 @@
TermID Name Value LogSize Frequency Uniqueness Dispensability Representative
-"GO:0000322" "storage vacuole" -3.996407586417781 5.029793525850104 0.2661182824452727 0.8555104067946925 0.12655094 null
-"GO:0005737" "cytoplasm" -2.421761796101055 7.238956814544198 43.076660800468886 0.8888902750046057 0.08859538 null
-"GO:0005852" "eukaryotic translation initiation factor 3 complex" -2.840897860731786 4.537264858754543 0.08561256229366826 0.6744908630409379 0.22333355 null
-"GO:0022625" "cytosolic large ribosomal subunit" -12.113076227493746 5.610954914935405 1.014469728138433 0.33018935796424503 0 null
-"GO:0022627" "cytosolic small ribosomal subunit" -2.3628115636350517 5.314539224168974 0.5126516507707168 0.35523486736625104 0.83441369 22625
-"GO:0044391" "ribosomal subunit" -6.05324848933085 5.901851569419728 1.9821488551869784 0.32421904182325845 0.83207123 22625
-"GO:0030687" "preribosome, large subunit precursor" -4.0721192326205085 4.726580518201694 0.1323907395608457 0.4963716015302116 0.53614612 null
-"GO:1990904" "ribonucleoprotein complex" -3.3638802864553807 6.239780566048521 4.315842197772249 0.6093677891596602 0.33654169 null
+"GO:0000322" "storage vacuole" -3.996407586417781 4.805201710439948 0.1778201926099983 0.8428127851699823 0.12770953 null
+"GO:0005737" "cytoplasm" -2.421761796101055 7.116137368897206 36.38509412593251 0.8619152465722402 0.10701902 null
+"GO:0005852" "eukaryotic translation initiation factor 3 complex" -2.840897860731786 4.5545981742240045 0.09985555503264143 0.6456414810665522 0.23478132 null
+"GO:0022625" "cytosolic large ribosomal subunit" -12.113076227493746 5.3629195651410235 0.6422496099261846 0.34085524602774525 0 null
+"GO:0022627" "cytosolic small ribosomal subunit" -2.3628115636350517 5.098875518374249 0.3496698818458546 0.3615708066454031 0.84980024 22625
+"GO:0044391" "ribosomal subunit" -6.05324848933085 5.773268492313049 1.6521669390616007 0.3420516961913126 0.74995524 22625
+"GO:0030687" "preribosome, large subunit precursor" -4.0721192326205085 4.562923026436936 0.10178817133005495 0.5094292084898253 0.50042336 null
+"GO:1990904" "ribonucleoprotein complex" -3.3638802864553807 6.19831198812342 4.396406893146647 0.592507283898729 0.34351463 null
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_treemap.pdf b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_treemap.pdf
index d21465b..74156f5 100644
Binary files a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_treemap.pdf and b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_CC_treemap.pdf differ
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_Rscript.R b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_Rscript.R
index c15ce0e..c88ad4b 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_Rscript.R
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_Rscript.R
@@ -19,17 +19,17 @@ library(treemap) # treemap package by Martijn Tennekes
# Here is your data from Revigo. Scroll down for plot configuration options.
revigo.names <- c("term_ID","description","frequency","value","uniqueness","dispensability","representative");
-revigo.data <- rbind(c("GO:0003735","structural constituent of ribosome",2.128498588986873,2.3063453870079487,1,-0,"structural constituent of ribosome"),
-c("GO:0003955","NAD(P)H dehydrogenase (quinone) activity",0.32041890398799755,5.946673441464065,0.7400056158989043,0.03782958,"NAD(P)H dehydrogenase (quinone) activity"),
-c("GO:0016765","transferase activity, transferring alkyl or aryl (other than methyl) groups",0.9927517685284755,14.124351859826227,0.9772580570277989,0,"transferase activity, transferring alkyl or aryl (other than methyl) groups"),
-c("GO:0016846","carbon-sulfur lyase activity",0.2130833609374284,2.6890263909525376,0.9794484639599235,0.03639583,"carbon-sulfur lyase activity"),
-c("GO:0019843","rRNA binding",1.1153325776412018,6.900720816804705,0.835202566885766,0.05274861,"rRNA binding"),
-c("GO:0003723","RNA binding",6.099813894661886,2.125599608641549,0.8072398915118998,0.3443017,"rRNA binding"),
-c("GO:0003743","translation initiation factor activity",0.37315089336372126,2.506156090153474,0.7572032240364351,0.24893209,"rRNA binding"),
-c("GO:0051540","metal cluster binding",1.944298077570841,12.725269847452662,0.8954228081211022,-0,"metal cluster binding"),
-c("GO:0051539","4 iron, 4 sulfur cluster binding",1.062682635515558,2.054019641899559,0.9024681871410898,0.15455964,"metal cluster binding"),
-c("GO:1901363","heterocyclic compound binding",20.072278748835316,2.125599608641549,0.8620729997677683,0.23645146,"metal cluster binding"),
-c("GO:0097159","organic cyclic compound binding",39.22969739688024,2.0791220405935267,0.8960665321996599,0.09126372,"organic cyclic compound binding"));
+revigo.data <- rbind(c("GO:0003735","structural constituent of ribosome",2.1449279465042137,2.3063453870079487,1,-0,"structural constituent of ribosome"),
+c("GO:0003955","NAD(P)H dehydrogenase (quinone) activity",0.043530454831469736,5.946673441464065,0.773019403110879,0.0306045,"NAD(P)H dehydrogenase (quinone) activity"),
+c("GO:0016765","transferase activity, transferring alkyl or aryl (other than methyl) groups",0.9423254583845189,14.124351859826227,0.9793855026034232,0,"transferase activity, transferring alkyl or aryl (other than methyl) groups"),
+c("GO:0016846","carbon-sulfur lyase activity",0.16052495238991618,2.6890263909525376,0.9814590528802952,0.03420288,"carbon-sulfur lyase activity"),
+c("GO:0019843","rRNA binding",1.0954409716541849,6.900720816804705,0.8327836646557257,0.05469995,"rRNA binding"),
+c("GO:0003723","RNA binding",5.722212435765044,2.125599608641549,0.8052553378367568,0.34544739,"rRNA binding"),
+c("GO:0003743","translation initiation factor activity",0.385996278395293,2.506156090153474,0.7534591290723279,0.25296266,"rRNA binding"),
+c("GO:0051540","metal cluster binding",1.9773485526914547,12.725269847452662,0.895217867426396,-0,"metal cluster binding"),
+c("GO:0051539","4 iron, 4 sulfur cluster binding",1.0717380484734336,2.054019641899559,0.902421624405444,0.1503654,"metal cluster binding"),
+c("GO:1901363","heterocyclic compound binding",20.31779257334349,2.125599608641549,0.8612069837988088,0.230554,"metal cluster binding"),
+c("GO:0097159","organic cyclic compound binding",39.169633533373776,2.0791220405935267,0.8924849646911944,0.09495105,"organic cyclic compound binding"));
stuff <- data.frame(revigo.data);
names(stuff) <- revigo.names;
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_TreeMap.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_TreeMap.tsv
index 482d19f..57dea59 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_TreeMap.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_TreeMap.tsv
@@ -3,14 +3,14 @@
# threshold to detect redundancies (c=0.10) and fill the 'representative' column, while normally c>=0.4 is recommended.
# To export a reduced-redundancy set of GO terms, go to the Scatterplot or Table tab, and export from there.
TermID Name Frequency Value Uniqueness Dispensability Representative
-"GO:0003735" "structural constituent of ribosome" 2.128498588986873 -2.3063453870079487 1 -0 null
-"GO:0003955" "NAD(P)H dehydrogenase (quinone) activity" 0.32041890398799755 -5.946673441464065 0.7400056158989043 0.03782958 null
-"GO:0016765" "transferase activity, transferring alkyl or aryl (other than methyl) groups" 0.9927517685284755 -14.124351859826227 0.9772580570277989 0 null
-"GO:0016846" "carbon-sulfur lyase activity" 0.2130833609374284 -2.6890263909525376 0.9794484639599235 0.03639583 null
-"GO:0019843" "rRNA binding" 1.1153325776412018 -6.900720816804705 0.835202566885766 0.05274861 null
-"GO:0003723" "RNA binding" 6.099813894661886 -2.125599608641549 0.8072398915118998 0.3443017 "rRNA binding"
-"GO:0003743" "translation initiation factor activity" 0.37315089336372126 -2.506156090153474 0.7572032240364351 0.24893209 "rRNA binding"
-"GO:0051540" "metal cluster binding" 1.944298077570841 -12.725269847452662 0.8954228081211022 -0 null
-"GO:0051539" "4 iron, 4 sulfur cluster binding" 1.062682635515558 -2.054019641899559 0.9024681871410898 0.15455964 "metal cluster binding"
-"GO:1901363" "heterocyclic compound binding" 20.072278748835316 -2.125599608641549 0.8620729997677683 0.23645146 "metal cluster binding"
-"GO:0097159" "organic cyclic compound binding" 39.22969739688024 -2.0791220405935267 0.8960665321996599 0.09126372 null
+"GO:0003735" "structural constituent of ribosome" 2.1449279465042137 -2.3063453870079487 1 -0 null
+"GO:0003955" "NAD(P)H dehydrogenase (quinone) activity" 0.043530454831469736 -5.946673441464065 0.773019403110879 0.0306045 null
+"GO:0016765" "transferase activity, transferring alkyl or aryl (other than methyl) groups" 0.9423254583845189 -14.124351859826227 0.9793855026034232 0 null
+"GO:0016846" "carbon-sulfur lyase activity" 0.16052495238991618 -2.6890263909525376 0.9814590528802952 0.03420288 null
+"GO:0019843" "rRNA binding" 1.0954409716541849 -6.900720816804705 0.8327836646557257 0.05469995 null
+"GO:0003723" "RNA binding" 5.722212435765044 -2.125599608641549 0.8052553378367568 0.34544739 "rRNA binding"
+"GO:0003743" "translation initiation factor activity" 0.385996278395293 -2.506156090153474 0.7534591290723279 0.25296266 "rRNA binding"
+"GO:0051540" "metal cluster binding" 1.9773485526914547 -12.725269847452662 0.895217867426396 -0 null
+"GO:0051539" "4 iron, 4 sulfur cluster binding" 1.0717380484734336 -2.054019641899559 0.902421624405444 0.1503654 "metal cluster binding"
+"GO:1901363" "heterocyclic compound binding" 20.31779257334349 -2.125599608641549 0.8612069837988088 0.230554 "metal cluster binding"
+"GO:0097159" "organic cyclic compound binding" 39.169633533373776 -2.0791220405935267 0.8924849646911944 0.09495105 null
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_barplot.png b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_barplot.png
deleted file mode 100644
index c34a1eb..0000000
Binary files a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_barplot.png and /dev/null differ
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_scatterPlot.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_scatterPlot.tsv
index 5b37fd4..30ee263 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_scatterPlot.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_scatterPlot.tsv
@@ -1,15 +1,15 @@
TermID Name Value LogSize Frequency Uniqueness Dispensability PC_0 PC_1 Representative
-"GO:0003723" "RNA binding" -2.125599608641549 6.43945443714506 6.099813894661886 0.8072398915118998 0.3443017 -4.666731731072316 -4.260299866573141 null
-"GO:0003735" "structural constituent of ribosome" -2.3063453870079487 5.982211513442491 2.128498588986873 1 -0 1.7486750480830981 5.038364273614814 null
-"GO:0003743" "translation initiation factor activity" -2.506156090153474 5.226024760921264 0.37315089336372126 0.7572032240364351 0.24893209 -5.524608601633725 -2.2345683688049425 null
-"GO:0090079" "translation regulator activity, nucleic acid binding" -2.0556205805954177 5.5575637407201075 0.8006170662803853 0.7484744077760994 0.9098599 null null 3743
-"GO:0003955" "NAD(P)H dehydrogenase (quinone) activity" -5.946673441464065 5.159858830504534 0.32041890398799755 0.7400056158989043 0.03782958 -2.0891378162748038 5.137735993228336 null
-"GO:0003954" "NADH dehydrogenase activity" -2.5031034455898045 5.186459068907396 0.34065796483880617 0.7525078358881252 0.84036841 null null 3955
-"GO:0008137" "NADH dehydrogenase (ubiquinone) activity" -3.210565435928671 4.982289328266 0.2128860040385874 0.742998513619593 0.90580117 null null 3955
-"GO:0016765" "transferase activity, transferring alkyl or aryl (other than methyl) groups" -14.124351859826227 5.6509793338587695 0.9927517685284755 0.9772580570277989 0 5.43067573000435 2.9565084544761597 null
-"GO:0016846" "carbon-sulfur lyase activity" -2.6890263909525376 4.982691752162833 0.2130833609374284 0.9794484639599235 0.03639583 -5.785297110330366 3.357387738602995 null
-"GO:0019843" "rRNA binding" -6.900720816804705 5.701542945487235 1.1153325776412018 0.835202566885766 0.05274861 -5.932827324719271 -3.864503916808567 null
-"GO:0051539" "4 iron, 4 sulfur cluster binding" -2.054019641899559 5.680542184778252 1.062682635515558 0.9024681871410898 0.15455964 4.192671653835016 -1.9056497399520858 null
-"GO:0051540" "metal cluster binding" -12.725269847452662 5.942901036457624 1.944298077570841 0.8954228081211022 -0 5.340396807981831 -4.234907668656025 null
-"GO:0097159" "organic cyclic compound binding" -2.0791220405935267 7.247752677084096 39.22969739688024 0.8960665321996599 0.09126372 -0.052562712520657764 -7.762331751295799 null
-"GO:1901363" "heterocyclic compound binding" -2.125599608641549 6.956734421862043 20.072278748835316 0.8620729997677683 0.23645146 3.1207150466652576 -5.089302558975814 null
+"GO:0003723" "RNA binding" -2.125599608641549 6.40046321177744 5.722212435765044 0.8052553378367568 0.34544739 4.68531525061372 -3.583394721577881 null
+"GO:0003735" "structural constituent of ribosome" -2.3063453870079487 5.974312230703925 2.1449279465042137 1 -0 -1.9947116687211122 5.4757273025583375 null
+"GO:0003743" "translation initiation factor activity" -2.506156090153474 5.2294847399952245 0.385996278395293 0.7534591290723279 0.25296266 5.560603405652529 -1.5425736458303276 null
+"GO:0090079" "translation regulator activity, nucleic acid binding" -2.0556205805954177 5.539427408845252 0.7880015875679078 0.7460395020846088 0.91511342 null null 3743
+"GO:0003955" "NAD(P)H dehydrogenase (quinone) activity" -5.946673441464065 4.281714970027296 0.043530454831469736 0.773019403110879 0.0306045 5.596128225185055 4.069385889214 null
+"GO:0003954" "NADH dehydrogenase activity" -2.5031034455898045 4.919971923220444 0.1892638364960708 0.7707388248007722 0.80762064 null null 3955
+"GO:0008137" "NADH dehydrogenase (ubiquinone) activity" -3.210565435928671 4.980539655506521 0.21758855662191656 0.7574406142483915 0.79795986 null null 3955
+"GO:0016765" "transferase activity, transferring alkyl or aryl (other than methyl) groups" -14.124351859826227 5.617101035413468 0.9423254583845189 0.9793855026034232 0 1.8367366280568642 5.718253810785204 null
+"GO:0016846" "carbon-sulfur lyase activity" -2.6890263909525376 4.8484477685814085 0.16052495238991618 0.9814590528802952 0.03420288 -5.602206748920797 3.2677659188722883 null
+"GO:0019843" "rRNA binding" -6.900720816804705 5.6824889447715865 1.0954409716541849 0.8327836646557257 0.05469995 5.989462551545925 -3.137818612884626 null
+"GO:0051539" "4 iron, 4 sulfur cluster binding" -2.054019641899559 5.6729886335160264 1.0717380484734336 0.902421624405444 0.1503654 -4.263271250987746 -1.4976500339425947 null
+"GO:0051540" "metal cluster binding" -12.725269847452662 5.938982792374914 1.9773485526914547 0.895217867426396 -0 -5.241541107856887 -3.9853020621047883 null
+"GO:0097159" "organic cyclic compound binding" -2.0791220405935267 7.235848595807177 39.169633533373776 0.8924849646911944 0.09495105 0.26248704132250256 -7.205738931045519 null
+"GO:1901363" "heterocyclic compound binding" -2.125599608641549 6.950775633109688 20.31779257334349 0.8612069837988088 0.230554 -2.8957663628188155 -4.718527957412137 null
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_table.tsv b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_table.tsv
index 7155cbf..73db85e 100644
--- a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_table.tsv
+++ b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_table.tsv
@@ -1,15 +1,15 @@
TermID Name Value LogSize Frequency Uniqueness Dispensability Representative
-"GO:0003723" "RNA binding" -2.125599608641549 6.43945443714506 6.099813894661886 0.8072398915118998 0.3443017 null
-"GO:0003735" "structural constituent of ribosome" -2.3063453870079487 5.982211513442491 2.128498588986873 1 -0 null
-"GO:0003743" "translation initiation factor activity" -2.506156090153474 5.226024760921264 0.37315089336372126 0.7572032240364351 0.24893209 null
-"GO:0090079" "translation regulator activity, nucleic acid binding" -2.0556205805954177 5.5575637407201075 0.8006170662803853 0.7484744077760994 0.9098599 3743
-"GO:0003955" "NAD(P)H dehydrogenase (quinone) activity" -5.946673441464065 5.159858830504534 0.32041890398799755 0.7400056158989043 0.03782958 null
-"GO:0003954" "NADH dehydrogenase activity" -2.5031034455898045 5.186459068907396 0.34065796483880617 0.7525078358881252 0.84036841 3955
-"GO:0008137" "NADH dehydrogenase (ubiquinone) activity" -3.210565435928671 4.982289328266 0.2128860040385874 0.742998513619593 0.90580117 3955
-"GO:0016765" "transferase activity, transferring alkyl or aryl (other than methyl) groups" -14.124351859826227 5.6509793338587695 0.9927517685284755 0.9772580570277989 0 null
-"GO:0016846" "carbon-sulfur lyase activity" -2.6890263909525376 4.982691752162833 0.2130833609374284 0.9794484639599235 0.03639583 null
-"GO:0019843" "rRNA binding" -6.900720816804705 5.701542945487235 1.1153325776412018 0.835202566885766 0.05274861 null
-"GO:0051539" "4 iron, 4 sulfur cluster binding" -2.054019641899559 5.680542184778252 1.062682635515558 0.9024681871410898 0.15455964 null
-"GO:0051540" "metal cluster binding" -12.725269847452662 5.942901036457624 1.944298077570841 0.8954228081211022 -0 null
-"GO:0097159" "organic cyclic compound binding" -2.0791220405935267 7.247752677084096 39.22969739688024 0.8960665321996599 0.09126372 null
-"GO:1901363" "heterocyclic compound binding" -2.125599608641549 6.956734421862043 20.072278748835316 0.8620729997677683 0.23645146 null
+"GO:0003723" "RNA binding" -2.125599608641549 6.40046321177744 5.722212435765044 0.8052553378367568 0.34544739 null
+"GO:0003735" "structural constituent of ribosome" -2.3063453870079487 5.974312230703925 2.1449279465042137 1 -0 null
+"GO:0003743" "translation initiation factor activity" -2.506156090153474 5.2294847399952245 0.385996278395293 0.7534591290723279 0.25296266 null
+"GO:0090079" "translation regulator activity, nucleic acid binding" -2.0556205805954177 5.539427408845252 0.7880015875679078 0.7460395020846088 0.91511342 3743
+"GO:0003955" "NAD(P)H dehydrogenase (quinone) activity" -5.946673441464065 4.281714970027296 0.043530454831469736 0.773019403110879 0.0306045 null
+"GO:0003954" "NADH dehydrogenase activity" -2.5031034455898045 4.919971923220444 0.1892638364960708 0.7707388248007722 0.80762064 3955
+"GO:0008137" "NADH dehydrogenase (ubiquinone) activity" -3.210565435928671 4.980539655506521 0.21758855662191656 0.7574406142483915 0.79795986 3955
+"GO:0016765" "transferase activity, transferring alkyl or aryl (other than methyl) groups" -14.124351859826227 5.617101035413468 0.9423254583845189 0.9793855026034232 0 null
+"GO:0016846" "carbon-sulfur lyase activity" -2.6890263909525376 4.8484477685814085 0.16052495238991618 0.9814590528802952 0.03420288 null
+"GO:0019843" "rRNA binding" -6.900720816804705 5.6824889447715865 1.0954409716541849 0.8327836646557257 0.05469995 null
+"GO:0051539" "4 iron, 4 sulfur cluster binding" -2.054019641899559 5.6729886335160264 1.0717380484734336 0.902421624405444 0.1503654 null
+"GO:0051540" "metal cluster binding" -12.725269847452662 5.938982792374914 1.9773485526914547 0.895217867426396 -0 null
+"GO:0097159" "organic cyclic compound binding" -2.0791220405935267 7.235848595807177 39.169633533373776 0.8924849646911944 0.09495105 null
+"GO:1901363" "heterocyclic compound binding" -2.125599608641549 6.950775633109688 20.31779257334349 0.8612069837988088 0.230554 null
diff --git a/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_treemap.pdf b/examples/output/aa/aa.candidates/results_revigo/aa.candidates_0.01_IDs_Pvalues_MF_treemap.pdf
index 7db00da..8a12144 100644
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