modularized sample coloring

.gitignore

@@ -1,4 +1,4 @@
-trees/metadata used for development
+# trees/metadata used for development
 data/
 
 # NodeJS file used for chrome headless QUnit tests

empress/empress-biom.py

@@ -14,8 +14,8 @@
 from tree import Tree
 
 # create/parse tree
-# tree_file = 'data/97_sites.nwk'
-tree_file = 'data/97_otus_no_none.tree'
+tree_file = 'data/97_sites.nwk'
+# tree_file = 'data/97_otus_no_none.tree'
 with open(tree_file) as file:
     nwk = file.readline();
 t = parse_newick(nwk)

empress/support_files/js/biom-table.js

@@ -1,83 +1,95 @@
 define([], function() {
-/**
- * biom-table
- */
-function BiomTable(obs, samp) {
     /**
-     * The observation table format:
-     * {sampleID1: [observationIDs],
-        sampleID2: [observationIDs],
-        ...}
-     * @private
+     * biom-table
      */
-    this._obs = obs;
+    function BiomTable(obs, samp) {
+        /**
+         * The observation table format:
+         * {sampleID1: [observationIDs],
+            sampleID2: [observationIDs],
+            ...}
+         * @private
+         */
+        this._obs = obs;
+
+        /**
+         * @type {Dictionary}
+         * Sample metedata format:
+         * {sampleID1: {cat1: val, cat2: val, ...},
+            sampleID2: {cat1: val, cat2: val, ...},
+            ...}
+         * @private
+         */
+        this._samp = samp;
+    };
 
     /**
-     * @type {Dictionary}
-     * Sample metedata format:
-     * {sampleID1: {cat1: val, cat2: val, ...},
-        sampleID2: {cat1: val, cat2: val, ...},
-        ...}
-     * @private
+     * Returns the list of observations in the sample
+     *
+     * @param {String} The sample Id
+     *
+     * @return {Array}
      */
-    this._samp = samp;
-};
+    BiomTable.prototype.getSampleObs = function(sId) {
+        var result = new Set();
+        return this._obs[sId];
+    };
 
-/**
- * Returns a dictionary of observation ids whose keys are the values of a sample
- * category.
- *
- * @param {String} The category to return observation
- *
- * @return {Dictionary}
- */
-BiomTable.prototype.getObsBy = function(cat) {
-    var result = {};
-    var cVal;
-    for (var sample in this._samp) {
-        cVal = this._samp[sample][cat];
-        if (!(cVal in result)) {
-            result[cVal] = new Set();
-        }
-        for (var i = 0; i < this._obs[sample].length; i++) {
-            result[cVal].add(this._obs[sample][i]);
+    /**
+     * Returns a dictionary of observation ids whose keys are the values of a sample
+     * category.
+     *
+     * @param {String} The category to return observation
+     *
+     * @return {Dictionary}
+     */
+    BiomTable.prototype.getObsBy = function(cat) {
+        var result = {};
+        var cVal;
+        for (var sample in this._samp) {
+            cVal = this._samp[sample][cat];
+            if (!(cVal in result)) {
+                result[cVal] = new Set();
+            }
+            for (var i = 0; i < this._obs[sample].length; i++) {
+                result[cVal].add(this._obs[sample][i]);
+            }
         }
-    }
 
-    for (var key in result) {
-        result[key] = Array.from(result[key]);
-    }
+        for (var key in result) {
+            result[key] = Array.from(result[key]);
+        }
 
-    return result;
-};
+        return result;
+    };
 
-/**
- * Returns number of unique observations in samples.
- *
- * @return {Number}
- */
-BiomTable.prototype.getUniqueObs = function() {
-    var obs = new Set();
+    /**
+     * Returns number of unique observations in samples.
+     *
+     * @return {Number}
+     */
+    BiomTable.prototype.getUniqueObs = function() {
+        var obs = new Set();
 
-    for (var sample in this._samp) {
-        for (var i = 0; i < this._obs[sample].length; i++) {
-            obs.add(this._obs[sample][i]);
+        for (var sample in this._samp) {
+            for (var i = 0; i < this._obs[sample].length; i++) {
+                obs.add(this._obs[sample][i]);
+            }
         }
-    }
 
-    return obs.size;
-};
+        return obs.size;
+    };
 
 
 
-/**
- * Returns a list of sample categories
- *
- * @return{Array}
- */
-BiomTable.prototype.getSampleCats = function() {
-    return Object.keys((Object.values(this._samp)[0])).sort();
-};
+    /**
+     * Returns a list of sample categories
+     *
+     * @return{Array}
+     */
+    BiomTable.prototype.getSampleCats = function() {
+        return Object.keys((Object.values(this._samp)[0])).sort();
+    };
 
  return BiomTable;
 });

empress/support_files/js/empress.js

@@ -6,9 +6,7 @@ define(['Camera', 'Drawer', 'Colorer', 'VectorOps'],
     const BLUE = 2;
 
     /**
-     *
      * @class EmpressTree
-     *
      */
     function Empress(tree, treeData, biom, pToName, canvas ) {
         /**
@@ -223,6 +221,20 @@ define(['Camera', 'Drawer', 'Colorer', 'VectorOps'],
         this._drawer.loadSampleThickBuf(coords);
     }
 
+    /**
+     * Color the tree by sample IDs
+     *
+     * @param {Array} sID - The sample IDs
+     * @param {Array} rgb - The rgb array which defines the color
+     */
+    Empress.prototype.colorSampleIDs = function(sIds, rgb) {
+        var tree = this._tree;
+        var obs = this._biom.getSampleObs(sIds);
+        for (var i = 0; i < obs.length; i++) {
+            this._treeData[obs].color = rgb;
+        }
+    };
+
     /**
      * Color the tree using sample data
      *
@@ -231,7 +243,7 @@ define(['Camera', 'Drawer', 'Colorer', 'VectorOps'],
      *
      * @return {dictionary} Maps keys to colors
      */
-    Empress.prototype.colorBySample = function(cat, color) {
+    Empress.prototype.colorBySampleCat = function(cat, color) {
         var tree = this._tree;
         var obs = this._biom.getObsBy(cat);
         var primes = [2, 3, 5, 7];
@@ -316,22 +328,16 @@ define(['Camera', 'Drawer', 'Colorer', 'VectorOps'],
         return keyInfo;
     };
 
-    // Empress.prototype.getSampleKeyInfo = function(cat) {
-
-    // };
-
     /**
      * Sets the color of the tree back to default
      */
     Empress.prototype.resetTree = function() {
         var keys = Object.keys(this._treeData);
         for (var i = 0; i < keys.length; i++) {
             var key = keys[i];
-            this._treeData[key].color = this.DEFAULT_COLOR;
-            // this._treeData[key].sampVal = this.DEFAULT_BRANCH_VAL;
-            this._treeData[key].visible = true;
+            this._treeData[key].color = this.DEFAULT_COLOR;                                                                                         this._treeData[key].visible = true;
         }
-        // this._drawer.loadSampleThickBuf([]);
+        this._drawer.loadSampleThickBuf([]);
     };
 
     /**

empress/support_files/js/side-panel-handler.js

@@ -155,7 +155,7 @@ define(['Colorer'], function(Colorer) {
         var colBy = this.sSel.value;
         var col = this.sColor.value;
         var hide = this.sHideChk.checked;
-        var keyInfo = this.empress.colorBySample(colBy, col);
+        var keyInfo = this.empress.colorBySampleCat(colBy, col);
         this.empress.hideUnColoredTips(hide);
         this.legend.addColorKey(colBy, keyInfo, 'node', false);
     };