Support rectangular (and arbitrarily configurable) layouts; minor typo fixes / detail additions in CLI

empress/_plot.py

@@ -48,19 +48,29 @@ def plot(output_dir: str,
     tools.name_internal_nodes(empress_tree)
 
     # TODO: figure out implications of screen size
-    empress_tree.coords(4020, 4020)
+    layout_to_coordsuffix, default_layout = empress_tree.coords(4020, 4020)
 
     tree_data = {}
     names_to_keys = {}
     for i, node in enumerate(empress_tree.postorder(include_self=True), 1):
         tree_data[i] = {
             'name': node.name,
-            'x': node.x2,
-            'y': node.y2,
             'color': [0.75, 0.75, 0.75],
             'sampVal': 1,
             'visible': True,
-            'single_samp': False}
+            'single_samp': False
+        }
+        # Add coordinate data from all layouts for this node
+        for layoutsuffix in layout_to_coordsuffix.values():
+            xcoord = "x" + layoutsuffix
+            ycoord = "y" + layoutsuffix
+            tree_data[i][xcoord] = getattr(node, xcoord)
+            tree_data[i][ycoord] = getattr(node, ycoord)
+        # Also add vertical bar coordinate info for the rectangular layout
+        if not node.is_tip():
+            tree_data[i]["highestchildyr"] = node.highestchildyr
+            tree_data[i]["lowestchildyr"] = node.lowestchildyr
+
         if node.name in names_to_keys:
             names_to_keys[node.name].append(i)
         else:
@@ -93,6 +103,8 @@ def plot(output_dir: str,
         'sample_data': sample_data,
         'obs_data': obs_data,
         'names': names,
+        'layout_to_coordsuffix': layout_to_coordsuffix,
+        'default_layout': default_layout,
         })
 
     copytree(SUPPORT_FILES, os.path.join(output_dir, 'support_files'))

empress/plugin_setup.py

@@ -16,19 +16,14 @@
 import pkg_resources
 __version__ = pkg_resources.get_distribution('empress').version  # noqa
 
-PARAMETERS = {'metadata': Metadata}
-PARAMETERS_DESC = {
-    'metadata': 'The sample metadata.'
-}
-
 plugin = Plugin(
     name='empress',
     version=__version__,
     website='http://github.com/biocore/empress',
     package='empress',
     citations=Citations.load('citations.bib', package='empress'),
     description=('This QIIME 2 plugin wraps Empress and '
-                 'supports interactive visualization of phylogentic '
+                 'supports interactive visualization of phylogenetic '
                  'trees.'),
     short_description='Plugin for visualizing phylogenies with Empress.'
 )
@@ -44,14 +39,26 @@
         'feature_metadata': Metadata
     },
     input_descriptions={
-        'tree': 'The phylogentic tree to visualize.',
-        'feature_table': 'The feature table to decorate the phylogeny.'
+        'tree': 'The phylogenetic tree to visualize.',
+        'feature_table': (
+            'The feature table relating samples to features in the tree. '
+            'This information allows us to decorate the phylogeny by '
+            'sample metadata.'
+        )
     },
     parameter_descriptions={
-        'sample_metadata': 'The sample metadata',
-        'feature_metadata': 'The feature metadata',
+        'sample_metadata': (
+            'Sample metadata. Can be used to color tips in the tree by '
+            'the samples they are unique to.'
+        ),
+        'feature_metadata': (
+            'Feature metadata. Not currently used for anything, but will '
+            'be soon.'
+        )
     },
     name='Visualize and Explore Phylogenies with Empress',
-    description='Generates an interactive phylgentic tree where the user '
-                'can visually integrate sample and feature metadata. '
+    description=(
+        'Generates an interactive phylogenetic tree visualization '
+        'supporting interaction with sample and feature metadata.'
+    )
 )

empress/support_files/js/biom-table.js

@@ -1,4 +1,4 @@
-define([], function() {
+define([], function () {
     /**
      * @class BIOM-table
      *
@@ -44,7 +44,7 @@ define([], function() {
      *
      * @return {Array}
      */
-    BIOMTable.convertToObs = function(countArray, obsIDs) {
+    BIOMTable.convertToObs = function (countArray, obsIDs) {
         var obs = [];
         for (var i = 0; i < countArray.length; i++) {
             if (countArray[i] != 0) {
@@ -61,9 +61,9 @@ define([], function() {
      *
      * @return {Array}
      */
-    BIOMTable.prototype.getObjservationUnionForSamples = function(sIds) {
+    BIOMTable.prototype.getObjservationUnionForSamples = function (sIds) {
         var result = new Set();
-        var addToResult = function(ob) {
+        var addToResult = function (ob) {
             result.add(ob);
         };
         for (var i = 0; i < sIds.length; i++) {
@@ -81,7 +81,7 @@ define([], function() {
      *
      * @return {Dictionary}
      */
-    BIOMTable.prototype.getObsBy = function(cat) {
+    BIOMTable.prototype.getObsBy = function (cat) {
         var result = {};
         var cVal;
         for (var sample in this._samp) {
@@ -106,7 +106,7 @@ define([], function() {
      *
      * @return {Number}
      */
-    BIOMTable.prototype.getObservations = function() {
+    BIOMTable.prototype.getObservations = function () {
         var obs = new Set();
 
         for (var sample in this._samp) {
@@ -123,7 +123,7 @@ define([], function() {
      *
      * @return{Array}
      */
-    BIOMTable.prototype.getSampleCategories = function() {
+    BIOMTable.prototype.getSampleCategories = function () {
         return Object.keys(Object.values(this._samp)[0]).sort();
     };
 

empress/support_files/js/bp-tree.js

@@ -1,4 +1,4 @@
-define(["ByteArray"], function(ByteArray) {
+define(["ByteArray"], function (ByteArray) {
     /**
      *
      * @class BPTree
@@ -123,7 +123,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return{Number}
      */
-    BPTree.prototype.rank = function(t, i) {
+    BPTree.prototype.rank = function (t, i) {
         var rCache = t ? this.r1Cache_ : this.r0Cache_;
         return rCache[i];
     };
@@ -138,7 +138,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return{Number}
      */
-    BPTree.prototype.select = function(t, k) {
+    BPTree.prototype.select = function (t, k) {
         var sCache = t ? this.s1Cache_ : this.s0Cache_;
         return sCache[k - 1];
     };
@@ -153,7 +153,7 @@ define(["ByteArray"], function(ByteArray) {
      * @return{Number} The excess at position i
      * @private
      */
-    BPTree.prototype.excess_ = function(i) {
+    BPTree.prototype.excess_ = function (i) {
         // need to subtract 1 since i starts at 0
         // Note: rank(1,i) - rank(0,i) = (2*(rank(1,i)) - i
         return 2 * this.r1Cache_[i] - i - 1;
@@ -167,7 +167,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return{Number} Depth of node i
      */
-    BPTree.prototype.depth = function(i) {
+    BPTree.prototype.depth = function (i) {
         //depth is same as excess
         return this.eCache_[i];
     };
@@ -180,7 +180,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return{String}
      */
-    BPTree.prototype.name = function(i) {
+    BPTree.prototype.name = function (i) {
         return this.names_[this.preorder(i) - 1];
     };
 
@@ -190,7 +190,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.numleafs = function() {
+    BPTree.prototype.numleafs = function () {
         var total = 0;
         for (var i = 0; i < this.b_.length - 1; i++) {
             total = this.isleaf(i) ? total + 1 : total;
@@ -206,7 +206,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return{Number}
      */
-    BPTree.prototype.length = function(i) {
+    BPTree.prototype.length = function (i) {
         return this.lengths_[this.preorder(i) - 1];
     };
 
@@ -220,7 +220,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.fwdsearchNaive = function(i, d) {
+    BPTree.prototype.fwdsearchNaive = function (i, d) {
         var b = this.eCache_[i] + d;
         for (var j = i + 1; i < this.b_.length; j++) {
             if (this.eCache_[j] === b) {
@@ -235,7 +235,7 @@ define(["ByteArray"], function(ByteArray) {
     /**
      * Currently this is just place holder
      */
-    BPTree.prototype.fwdsearch = function(i, d) {
+    BPTree.prototype.fwdsearch = function (i, d) {
         return this.fwdsearchNaive(i, d);
     };
 
@@ -249,7 +249,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.bwdsearchNaive = function(i, d) {
+    BPTree.prototype.bwdsearchNaive = function (i, d) {
         var b = this.eCache_[i] + d;
         for (var j = i - 1; j >= 0; j--) {
             if (this.eCache_[j] === b) {
@@ -264,7 +264,7 @@ define(["ByteArray"], function(ByteArray) {
     /**
      * Currently this is just a place holder
      */
-    BPTree.prototype.bwdsearch = function(i, d) {
+    BPTree.prototype.bwdsearch = function (i, d) {
         return this.bwdsearchNaive(i, d);
     };
 
@@ -276,7 +276,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.open = function(i) {
+    BPTree.prototype.open = function (i) {
         return this.b_[i] ? i : this.ocCache_[i];
     };
 
@@ -288,7 +288,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.close = function(i) {
+    BPTree.prototype.close = function (i) {
         return this.b_[i] ? this.ocCache_[i] : i;
     };
 
@@ -300,7 +300,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.enclose = function(i) {
+    BPTree.prototype.enclose = function (i) {
         // i is an open paren
         if (this.b_[i]) {
             return this.bwdsearch(i, -2) + 1;
@@ -319,7 +319,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.parent = function(i) {
+    BPTree.prototype.parent = function (i) {
         // i represents the root node
         if (i === this.root() || i === this.b_.length - 1) {
             return -1;
@@ -333,7 +333,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.root = function() {
+    BPTree.prototype.root = function () {
         return 0;
     };
 
@@ -342,7 +342,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {boolean}
      */
-    BPTree.prototype.isleaf = function(i) {
+    BPTree.prototype.isleaf = function (i) {
         return this.b_[i] && !this.b_[i + 1];
     };
 
@@ -354,7 +354,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number} return 0 if i is a leaf node
      */
-    BPTree.prototype.fchild = function(i) {
+    BPTree.prototype.fchild = function (i) {
         if (this.isleaf(i)) {
             return 0;
         }
@@ -373,7 +373,7 @@ define(["ByteArray"], function(ByteArray) {
      *                 i can be either an open or close parenthesis
      * @return {Number} return 0 if i is a leaf node
      */
-    BPTree.prototype.lchild = function(i) {
+    BPTree.prototype.lchild = function (i) {
         if (this.isleaf(i)) {
             return 0;
         }
@@ -393,7 +393,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number}
      */
-    BPTree.prototype.nsibling = function(i) {
+    BPTree.prototype.nsibling = function (i) {
         // i is a close parenthesis
         if (!this.b_[i]) {
             return this.nsibling(this.open(i));
@@ -419,7 +419,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number} returns 0 if no previous sibling
      */
-    BPTree.prototype.psibling = function(i) {
+    BPTree.prototype.psibling = function (i) {
         var pos = 0;
 
         // check to see if i is root
@@ -459,7 +459,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number} The postorder rank of node i
      */
-    BPTree.prototype.postorder = function(i) {
+    BPTree.prototype.postorder = function (i) {
         if (this.b_[i]) {
             return this.rank(0, this.close(i));
         } else {
@@ -475,7 +475,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number} The index position of the node in the tree
      */
-    BPTree.prototype.postorderselect = function(k) {
+    BPTree.prototype.postorderselect = function (k) {
         return this.open(this.select(0, k));
     };
 
@@ -486,7 +486,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number} The preorder rank of node i
      */
-    BPTree.prototype.preorder = function(i) {
+    BPTree.prototype.preorder = function (i) {
         if (this.b_[i]) {
             return this.rank(1, i);
         } else {
@@ -502,7 +502,7 @@ define(["ByteArray"], function(ByteArray) {
      *
      * @return {Number} The index position of the node in the tree
      */
-    BPTree.prototype.preorderselect = function(k) {
+    BPTree.prototype.preorderselect = function (k) {
         return this.select(1, k);
     };