Add more projection methods

app/assets/javascripts/fn/complex/lalolib.js

@@ -1,6 +1,30 @@
 fn.lalolib     = {}; // These interact with the LALOLib structures directly.
 fn.lalolib.svd = {}; // For dealing with SVD
 
+/**
+ * Scales columns of the matrix from 0 to 1.
+ *
+ * TODO needs specs.
+ *
+ * @param M
+ * @returns {returns}
+ */
+fn.lalolib.scale_cols_from_0_to_1 = function (M) {
+  var func = function (col) {
+    var min     = fn.ary.min(col);
+    var max     = fn.ary.max(col);
+    var new_min = 0;
+    var new_max = 1;
+
+    return col.map(function (val) {
+      return fn.math.scale(val, min, max, new_min, new_max);
+    });
+  };
+
+  return fn.lalolib.apply_to_cols(M, func);
+};
+
+
 /**
  * Applies the func to each col in the Matrix M.
  *
@@ -296,7 +320,7 @@ fn.lalolib.svd.svd = function (M, center) {
       numeric_svd    = null;
 
   try {
-    svd = lalolib.svd(the_matrix, "thinU");
+    svd = lalolib.svd(the_matrix, "full");
   }
   catch (error) {
     console.log("lalolib.svd() failed with error: " + error + ".  Trying numeric.svd() instead.");
@@ -312,7 +336,7 @@ fn.lalolib.svd.svd = function (M, center) {
       svd = {
         S: lalolib.array2mat(numeric.diag(numeric_svd.S)),
         U: lalolib.array2mat(numeric_svd.V),
-        V: undefined,
+        V: lalolib.array2mat(numeric_svd.U),
         s: lalolib.array2mat(numeric_svd.S)
       };
     }
@@ -324,7 +348,7 @@ fn.lalolib.svd.svd = function (M, center) {
       svd = {
         S: lalolib.array2mat(numeric.diag(numeric_svd.S)),
         U: lalolib.array2mat(numeric_svd.U),
-        V: undefined,
+        V: lalolib.array2mat(numeric_svd.V),
         s: lalolib.array2mat(numeric_svd.S)
       };
     }

app/assets/javascripts/fn/complex/parsed_biom.js

@@ -972,14 +972,17 @@ fn.parsed_biom.new = function (params) {
   // fully_parsed_biom.count_matrix = fn.parsed_biom.count_matrix(fully_parsed_biom.leaf_names, fully_parsed_biom.counts_for_each_leaf);
   fully_parsed_biom.count_matrix = fn.parsed_biom.count_matrix(fully_parsed_biom.leaf_names, fully_parsed_biom.counts_for_each_leaf);
 
-  fully_parsed_biom.projection = TODO;
+  fully_parsed_biom.projection = null;
   if (projection_type === "pc") {
     fully_parsed_biom.projection = fn.project.project_with_num_pcs_cutoff(fully_parsed_biom.count_matrix, sing_vals_to_keep);
   }
   else {
     fully_parsed_biom.projection = fn.project.project_with_variance_cutoff(fully_parsed_biom.count_matrix, sing_vals_to_keep);
   }
 
+  fully_parsed_biom.projection_leaves_1d = fn.project.projection_leaves_1d(fully_parsed_biom.count_matrix);
+  fully_parsed_biom.projection_samples_1d = fn.project.projection_samples_1d(fully_parsed_biom.count_matrix);
+
   return fully_parsed_biom;
 };
 

app/assets/javascripts/fn/complex/project.js

@@ -52,3 +52,31 @@ fn.project.project_with_num_pcs_cutoff = function (M, num_pcs_to_keep) {
     return fn.lalolib.first_n_cols(pca_scores, num_pcs_to_keep);
   }
 };
+
+/**
+ * Return a 1D projection of the samples in PC space.
+ *
+ * The output is scaled from 0 to 1 for use in the chroma.js color scale functions.
+ *
+ * @param M
+ * @returns {Matrix}
+ */
+fn.project.projection_samples_1d = function (M) {
+  var svd = fn.lalolib.svd.svd(M, true);
+
+  var scores = fn.lalolib.scale_cols_from_0_to_1(lalolib.mul(svd.V, svd.S));
+
+  return fn.lalolib.first_n_cols(scores, 1);
+};
+
+/**
+ * Return a 1D projection of leaves in PC space.
+ *
+ * The output is scaled from 0 to 1 for use in the chroma.js color scale functions.
+ *
+ * @param M
+ * @returns {Object}
+ */
+fn.project.projection_leaves_1d = function (M) {
+  return fn.lalolib.scale_cols_from_0_to_1(fn.project.project_with_num_pcs_cutoff(M, 1));
+};

spec/javascripts/fn.parsed_biom_spec.js

@@ -542,6 +542,15 @@ describe("fn", function () {
       it("sets projection", function () {
         spec_helper.expect_stringify_equal(actual.projection, expected.projection);
       });
+
+      it("sets projection_leaves_1d", function () {
+        spec_helper.expect_stringify_equal(actual.projection_leaves_1d, expected.projection_leaves_1d);
+      });
+
+      it("sets projection_samples_1d", function () {
+        // Note that actual is a 6x1 matrix, but the expected is just a vector, so take the val of actual.
+        spec_helper.expect_stringify_equal(actual.projection_samples_1d.val, expected.projection_samples_1d);
+      });
     });
   });
 });

spec/javascripts/spec_helper_functions.js

@@ -440,6 +440,14 @@ spec_helper.test_case.COUNT_MATRIX_PCA_SCORES = lalolib.mul(spec_helper.test_cas
 // The projection will give two singular values.
 spec_helper.test_case.PROJECTION = fn.lalolib.first_n_cols(spec_helper.test_case.COUNT_MATRIX_PCA_SCORES, 2);
 
+
+// These come from scaling the projection by hand
+spec_helper.test_case.PROJECTION_LEAVES_1D = lalolib.array2mat([
+  [1],
+  [0]
+]);
+spec_helper.test_case.PROJECTION_SAMPLES_1D = lalolib.array2mat([0.3333333333333333, 0.3333333333333333, 0.8333333333333334, 0, 1, 0.5]);
+
 spec_helper.test_case.COUNTS_WITH_ZEROS_REPLACED = {
   apple: [global.ZERO_REPLACEMENT_VAL, 1, 2, global.ZERO_REPLACEMENT_VAL, 3, 4],
   pie: [1, 2, global.ZERO_REPLACEMENT_VAL, 3, global.ZERO_REPLACEMENT_VAL, 4]
@@ -691,7 +699,10 @@ spec_helper.test_case.FULLY_PARSED_BIOM = {
   approx_starting_colors_html: spec_helper.test_case.APPROX_STARTING_COLORS_HTML,
 
   count_matrix: spec_helper.test_case.COUNT_MATRIX,
-  projection: spec_helper.test_case.PROJECTION
+  projection: spec_helper.test_case.PROJECTION,
+
+  projection_leaves_1d: spec_helper.test_case.PROJECTION_LEAVES_1D,
+  projection_samples_1d: spec_helper.test_case.PROJECTION_SAMPLES_1D
 };
 
 // See svd.r for how this was generated.