chromatography - npm Package Compare versions

Comparing version 1.2.0 to 2.0.0

package.json

 {
   "name": "chromatography",
-  "version": "1.2.0",
+  "version": "2.0.0",
   "description": "Tools for storing, search and analize GC/MS spectra",
@@ -54,9 +54,10 @@ "main": "src/index.js",
     "eslint-plugin-no-only-tests": "^1.1.0",
-    "jcampconverter": "^2.3.0",
     "nyc": "^8.3.0"
   },
   "dependencies": {
-    "ml-gsd": "mljs/global-spectral-deconvolution#peak-high",
+    "binary-search": "^1.3.2",
+    "jcampconverter": "^2.3.0",
+    "ml-gsd": "^2.0.1",
     "ml-regression": "^4.1.1"
   }
 }

README.md

@@ -9,3 +9,3 @@ # chromatography
 
-> Tools for storing, search and analize GC/MS spectra
+> Tools for storing, search and analyze GC/MS spectra
 
@@ -16,13 +16,28 @@ https://docs.google.com/document/d/1Jg2l6wKjFCYBSqdVWBSujSkqMhsEV6ZMyxeI9RSLhn0/edit#heading=h.8gjgl6jygt0s
 
-```bash
-npm install chromatography
-```
+`npm install chromatography`
 
 ## [API Documentation](https://cheminfo-js.github.io/chromatography/)
 
-## Test
+## Example
 
-```bash
-npm install
-npm test
+```js
+const GCMS = require('chromatography');
+let gcms = GCMS.fromJcamp(jcampReferenceMixture);
+
+let kovatsConversionTable = GCMS.getKovatsTable(gcms); // [{time, value}, ]
+let conversionFunction = GCMS.kovatsConversionFunction(kovatsConversionTable, {});
+
+let diesel = GCMS.fromJcamp(jcampOfDiesel);
+let times = GCMS.rescaleTime(diesel.getTimes(), conversionFunction);
+diesel.setTimes(times);
+// diesel.rescaleTime(conversionFunction);
+
+let peaks = GCMS.getPeaks(diesel, options);
+let dieselJSON = diesel.toJSON(options); // [ {time:12, height:12, width: 3, mass: [{mass, intensity}]} ]
+let gcms2 = GCMS.fromJSON(anotherDieselJSON);
+let similarity = GCMS.similarity(gcms, gcms2, options)
+
+// get a spectrum in another reference model
+let revertConversionFunction = GCMS.kovatsConversionFunction(kovatsConversionTable, {revert: true});
+let mySpectrumInAnotherReference = mySpectrum
 ```
@@ -29,0 +44,0 @@

src/Chromatogram.js

 'use strict';
 
+const rescaleTime = require('./rescaleTime');
+
 /**
@@ -7,3 +9,3 @@ * Class allowing to store time / ms (ms) series
  * @class Chromatogram
- * @param {Object|Array<Number>} data - A GC/MS data format object or a time serie
+ * @param {object|Array<number>} data - A GC/MS data format object or a time serie
  */
@@ -35,4 +37,4 @@ class Chromatogram {
      * Find the serie giving the name
-     * @param {String} name - name of the serie
-     * @return {Object} - Object with an array of data, dimensions of the elements in the array and name of the serie
+     * @param {string} name - name of the serie
+     * @return {object} - Object with an array of data, dimensions of the elements in the array and name of the serie
      */
@@ -45,3 +47,3 @@ findSerieByName(name) {
      * Add a new serie
-     * @param {Object} serie - Object with an array of data, dimensions of the elements in the array and name of the serie
+     * @param {object} serie - Object with an array of data, dimensions of the elements in the array and name of the serie
      */
@@ -66,3 +68,3 @@ addSerie(serie) {
      * Returns the first time value
-     * @return {Number} - First time value
+     * @return {number} - First time value
      */
@@ -75,3 +77,3 @@ getFirstTime() {
      * Returns the last time value
-     * @return {Number} - Last time value
+     * @return {number} - Last time value
      */
@@ -84,3 +86,3 @@ getLastTime() {
      * Returns the time values
-     * @return {Array<Number>} - Time values
+     * @return {Array<number>} - Time values
      */
@@ -90,4 +92,52 @@ getTimes() {
     }
+
+    /**
+     * Assign the time values
+     * @param {Array<number>} times - New time values
+     */
+    setTimes(times) {
+        this.times = times;
+    }
+
+    /**
+     * Modifies the time applying the conversion function
+     * @param {function(number)} conversionFunction
+     */
+    rescaleTime(conversionFunction) {
+        this.times = rescaleTime(this.times, conversionFunction);
+    }
+
+    /**
+     * Parse the content to an JSON Array
+     * @return {Array<object>} - Returns a list with the following fields:
+     *  * `time`: Number for the retention time
+     *  * `tic`: Number for the total ion chromatogram
+     *  * `mass`: List of mass values and their respective intensities
+     */
+    toJSON() {
+        var ans = new Array(this.times.length);
+        const tic = this.findSerieByName('tic').data;
+        const mass = this.findSerieByName('ms').data.map((ms) => {
+            var ansMS = new Array(ms[0].length);
+            for (var i = 0; i < ansMS.length; i++) {
+                ansMS[i] = {
+                    mass: ms[0][i],
+                    intensity: ms[1][i]
+                };
+            }
+            return ansMS;
+        });
+
+        for (var i = 0; i < ans.length; i++) {
+            ans[i] = {
+                time: this.times[i],
+                tic: tic[i],
+                mass: mass[i]
+            };
+        }
+
+        return ans;
+    }
 }
 
 module.exports = Chromatogram;

src/cosine.js

@@ -5,7 +5,7 @@ 'use strict';
  * Cosine similarity between two MS spectra
- * @param {Array<Number>} ms1x - Array of mass values for the first spectra
- * @param {Array<Number>} ms1y - Array of weighted abundance values for the first spectra
- * @param {Array<Number>} ms2x - Array of mass values for the second spectra
- * @param {Array<Number>} ms2y - Array of weighted abundance values for the second spectra
- * @return {Number} - Similarity between two MS spectra
+ * @param {Array<number>} ms1x - Array of mass values for the first spectra
+ * @param {Array<number>} ms1y - Array of weighted abundance values for the first spectra
+ * @param {Array<number>} ms2x - Array of mass values for the second spectra
+ * @param {Array<number>} ms2y - Array of weighted abundance values for the second spectra
+ * @return {number} - Similarity between two MS spectra
  */
@@ -12,0 +12,0 @@ function cosine(ms1x, ms1y, ms2x, ms2y) {

src/index.js

@@ -6,3 +6,3 @@ 'use strict';
 // Chromatography utils
-exports.peakPicking = require('./peakPicking');
+exports.getPeaks = require('./getPeaks');
 exports.massInPeaks = require('./massInPeaks');
@@ -15,1 +15,6 @@ exports.vectorify = require('./vectorify');
 exports.kovats = require('./kovats');
+exports.getKovatsTable = require('./getKovatsTable');
+exports.kovatsConversionFunction = require('./kovatsConversionFunction');
+exports.rescaleTime = require('./rescaleTime');
+exports.fromJcamp = require('./fromJcamp');
+exports.fromJSON = require('./fromJSON');

src/kovats.js

@@ -5,6 +5,6 @@ 'use strict';
  * Calculates the Kovats retention index for a mass spectra of a n-alkane
- * @param {Object} ms - An mass spectra object
- * @param {Array<Number>} ms.x - Array of masses
- * @param {Array<Number>} ms.y - Array of intensities
- * @return {Number} - Kovats retention index
+ * @param {object} ms - An mass spectra object
+ * @param {Array<number>} ms.x - Array of masses
+ * @param {Array<number>} ms.y - Array of intensities
+ * @return {number} - Kovats retention index
  */
@@ -11,0 +11,0 @@ function kovats(ms) {

src/massFilter.js

@@ -6,6 +6,6 @@ 'use strict';
  * @ignore
- * @param {Array<Object>} list - Sorted list of XY-objects to be filtered
- * @param {Number} maxNumberPeaks - Maximum number of peaks for each mass spectra
- * @param {Number} groupWidth - When find a max can't be another max in a radius of this size
- * @return {Array<Object>} - List of XY-objects filtered
+ * @param {Array<object>} list - Sorted list of XY-objects to be filtered
+ * @param {number} maxNumberPeaks - Maximum number of peaks for each mass spectra
+ * @param {number} groupWidth - When find a max can't be another max in a radius of this size
+ * @return {Array<object>} - List of XY-objects filtered
  */
@@ -35,10 +35,10 @@ function moreDistinct(list, maxNumberPeaks, groupWidth) {
  * Filters a mass object
- * @param {Object} massXYObject - Object with x and y data
- * @param {Array<Number>} massXYObject.x - Array of mass values
- * @param {Array<Number>} massXYObject.y - Array of abundance values
- * @param {Object} options - Options for the integral filtering
- * @param {Number} [options.thresholdFactor = 0] - Every peak that it's bellow the main peak times this factor fill be removed (when is 0 there's no filter)
- * @param {Number} [options.maxNumberPeaks = Number.MAX_VALUE] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
- * @param {Number} [options.groupWidth = 0] - When find a max can't be another max in a radius of this size
- * @return {Object} - Object with filtered x and y data
+ * @param {object} massXYObject - Object with x and y data
+ * @param {Array<number>} massXYObject.x - Array of mass values
+ * @param {Array<number>} massXYObject.y - Array of abundance values
+ * @param {object} options - Options for the integral filtering
+ * @param {number} [options.thresholdFactor = 0] - Every peak that it's bellow the main peak times this factor fill be removed (when is 0 there's no filter)
+ * @param {number} [options.maxNumberPeaks = Number.MAX_VALUE] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
+ * @param {number} [options.groupWidth = 0] - When find a max can't be another max in a radius of this size
+ * @return {object} - Object with filtered x and y data
  */
@@ -45,0 +45,0 @@ function massFilter(massXYObject, options = {}) {

src/massInPeaks.js

@@ -7,9 +7,9 @@ 'use strict';
  * Integrate MS spectra of a peak list
- * @param {Array<Object>} peakList - List of GSD objects
- * @param {Array<Object>} sampleMS - MS array of GC spectra
- * @param {Object} options - Options for the integral filtering
- * @param {Number} [options.thresholdFactor = 0] - Every peak that it's bellow the main peak times this factor fill be removed (when is 0 there's no filter)
- * @param {Number} [options.maxNumberPeaks = Number.MAX_VALUE] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
- * @param {Number} [options.groupWidth = 0] - When find a max can't be another max in a radius of this size
- * @return {Array<Object>} - List of GSD objects with an extra 'ms' field with the integrated MS spectra
+ * @param {Array<object>} peakList - List of GSD objects
+ * @param {Array<object>} sampleMS - MS array of GC spectra
+ * @param {object} options - Options for the integral filtering
+ * @param {number} [options.thresholdFactor = 0] - Every peak that it's bellow the main peak times this factor fill be removed (when is 0 there's no filter)
+ * @param {number} [options.maxNumberPeaks = Number.MAX_VALUE] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
+ * @param {number} [options.groupWidth = 0] - When find a max can't be another max in a radius of this size
+ * @return {Array<object>} - List of GSD objects with an extra 'ms' field with the integrated MS spectra
  */
@@ -16,0 +16,0 @@ function massInPeaks(peakList, sampleMS, options = {}) {

src/scaleAlignment.js

@@ -7,16 +7,15 @@ 'use strict';
  * Aligns the time of the sample based on the regression with his reference value
- * @param {Array<Object>} reference - Array of peaks, integrated mass spectra and weighted mass spectra for the reference chromatogram
- * @param {Array<Object>} sample - Array of peaks, integrated mass spectra and weighted mass spectra for the sample chromatogram
- * @param {Object} [options] - Options object
- * @param {Boolean} [options.computeQuality = false] - Calculate the quality of the regression
- * @param {Number} [options.stringFormula = 0] - Precision of the string formula (0 if don't need the value)
- * @param {Number} [options.polynomialDegree = 3] - Degree of the polynomial regression
- * @return {Object} - The scaled spectra:
- * * `reference`: The reference array
- * * `sample`: The scaled sample array
+ * @param {Array<object>} reference - Array of peaks, integrated mass spectra and weighted mass spectra for the reference chromatogram
+ * @param {Array<object>} sample - Array of peaks, integrated mass spectra and weighted mass spectra for the sample chromatogram
+ * @param {object} [options] - Options object
+ * @param {boolean} [options.computeQuality = false] - Calculate the quality of the regression
+ * @param {number} [options.polynomialDegree = 3] - Degree of the polynomial regression
+ * @return {object} - The scaled spectra:
+ * * `scaleRegression`: The regression function to make the regression
  * * `stringFormula`: Regression equation
  * * `r2`: R2 quality number
+ * * `error`: Vector of the difference between the spected value and the actual shift value
  */
 function scaleAlignment(reference, sample, options = {}) {
-    const {computeQuality = false, stringFormula = 0, polynomialDegree = 3} = options;
+    const {computeQuality = false, polynomialDegree = 3} = options;
     let referenceTime = reference.map((val) => val.x);
@@ -27,18 +26,14 @@ let sampleTime = sample.map((val) => val.x);
 
-    const maxTime = Math.max(...referenceTime);
-    let scaledSample = sample.map((peak) => {
-        peak.x = regression.predict(peak.x);
-        return peak;
-    }).filter((peak) => peak.x <= maxTime);
+    let error = new Array(sample.length);
+    for (var i = 0; i < sample.length; i++) {
+        error[i] = reference[i].x - regression.predict(sample[i].x);
+    }
 
     let ans = {
-        reference: reference,
-        sample: scaledSample
+        scaleRegression: regression
     };
 
-    if (stringFormula !== 0) {
-        ans.stringFormula = regression.toString(stringFormula);
-    }
     if (computeQuality) {
         ans.r2 = regression.quality.r2;
+        ans.error = error;
     }
@@ -45,0 +40,0 @@ return ans;

src/spectraComparison.js

 'use strict';
 
-const peakPicking = require('./peakPicking');
+const getPeaks = require('./getPeaks');
 const massInPeaks = require('./massInPeaks');
@@ -12,8 +12,8 @@ const vectorify = require('./vectorify');
  * @param {Chromatogram} chromatography - Chromatogram to process
- * @param {Object} [options] - Options object (same as spectraComparison)
- * @return {{peaks: Array<Object>, integratedMs: Array<Object>, vector: Array<Object>}} - Array of peaks, integrated mass spectra and weighted mass spectra
+ * @param {object} [options] - Options object (same as spectraComparison)
+ * @return {{peaks: Array<object>, integratedMs: Array<object>, vector: Array<object>}} - Array of peaks, integrated mass spectra and weighted mass spectra
  */
 function preprocessing(chromatography, options) {
     // peak picking
-    let peaks = peakPicking(chromatography, options);
+    let peaks = getPeaks(chromatography, options);
     peaks = peaks.sort((a, b) => a.index - b.index);
@@ -47,14 +47,14 @@
  * @param {Chromatogram} chrom2 - Second chromatogram
- * @param {Object} [options] - Options object
- * @param {Number} [options.thresholdFactor = 0] - Every peak that it's bellow the main peak times this factor fill be removed (when is 0 there's no filter)
- * @param {Number} [options.maxNumberPeaks = Number.MAX_VALUE] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
- * @param {Number} [options.groupWidth = 0] - When find a max can't be another max in a radius of this size
- * @param {Number} [options.heightFilter = 2] - Filter all objects that are bellow `heightFilter` times the median of the height
- * @param {Number} [options.massPower = 3] - Power applied to the mass values
- * @param {Number} [options.intPower = 0.6] - Power applied to the abundance values
- * @param {Number} [options.similarityThreshold = 0.7] - Minimum similarity value to consider them similar
- * @return {Object} - Most similar peaks and their similarities:
+ * @param {object} [options] - Options object
+ * @param {number} [options.thresholdFactor = 0] - Every peak that it's bellow the main peak times this factor fill be removed (when is 0 there's no filter)
+ * @param {number} [options.maxNumberPeaks = Number.MAX_VALUE] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
+ * @param {number} [options.groupWidth = 0] - When find a max can't be another max in a radius of this size
+ * @param {number} [options.heightFilter = 2] - Filter all objects that are bellow `heightFilter` times the median of the height
+ * @param {number} [options.massPower = 3] - Power applied to the mass values
+ * @param {number} [options.intPower = 0.6] - Power applied to the abundance values
+ * @param {number} [options.similarityThreshold = 0.7] - Minimum similarity value to consider them similar
+ * @return {object} - Most similar peaks and their similarities:
  * * `peaksFirst`: Array of peaks, integrated mass spectra and weighted mass spectra for the first chromatogram
  * * `peaksSecond`: Array of peaks, integrated mass spectra and weighted mass spectra for the second chromatogram
- * * `peaksSimilarity`: Array of similarities (Number)
+ * * `peaksSimilarity`: Array of similarities (number)
  */
@@ -106,3 +106,3 @@ function spectraComparison(chrom1, chrom2, options) {
     for (let i = 0; i < similarLen; ++i) {
-        if (duplicates.hasOwnProperty(similarityPeaks.chrom1[i].x)) {
+        if ({}.hasOwnProperty.call(duplicates, similarityPeaks.chrom1[i].x)) {
             duplicates[similarityPeaks.chrom1[i].x].push(i);
@@ -109,0 +109,0 @@ } else {

src/vectorify.js

@@ -7,10 +7,10 @@ 'use strict';
  * Given a list of GSD objects returns the weighted mass times abundance
- * @param {Array<Object>} peakList - List of GSD objects
- * @param {Object} options - Options for the integral filtering
- * @param {Number} [options.massPower = 3] - Power applied to the mass values
- * @param {Number} [options.intPower = 0.6] - Power applied to the abundance values
- * @param {Number} [options.thresholdFactor = 0] - Every peak that it's bellow the main peak times this factor fill be removed (when is 0 there's no filter)
- * @param {Number} [options.maxNumberPeaks = Number.MAX_VALUE] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
- * @param {Number} [options.groupWidth = 0] - When find a max can't be another max in a radius of this size
- * @return {Array<Object>} - List of mass and weighted mass times abundance objects
+ * @param {Array<object>} peakList - List of GSD objects
+ * @param {object} options - Options for the integral filtering
+ * @param {number} [options.massPower = 3] - Power applied to the mass values
+ * @param {number} [options.intPower = 0.6] - Power applied to the abundance values
+ * @param {number} [options.thresholdFactor = 0] - Every peak that it's bellow the main peak times this factor fill be removed (when is 0 there's no filter)
+ * @param {number} [options.maxNumberPeaks = Number.MAX_VALUE] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
+ * @param {number} [options.groupWidth = 0] - When find a max can't be another max in a radius of this size
+ * @return {Array<object>} - List of mass and weighted mass times abundance objects
  */
@@ -17,0 +17,0 @@ function vectorify(peakList, options = {}) {

test/cosine.js

@@ -6,3 +6,3 @@ import test from 'ava';
 import {join} from 'path';
-import {Chromatogram, massInPeaks, peakPicking, vectorify, cosine} from '..';
+import {Chromatogram, massInPeaks, getPeaks, vectorify, cosine} from '..';
 
@@ -23,3 +23,3 @@ const readFileAsync = Promise.promisify(fs.readFile);
 
-    let peakList = peakPicking(chrom);
+    let peakList = getPeaks(chrom);
     t.is(peakList.length, 312);
@@ -63,3 +63,3 @@
 
-    let peakList = peakPicking(chrom);
+    let peakList = getPeaks(chrom);
     t.is(peakList.length, 1);
@@ -66,0 +66,0 @@

test/loadJcamp.js

 import test from 'ava';
-import {convert} from 'jcampconverter';
 import fs from 'fs';
 import Promise from 'bluebird';
 import {join} from 'path';
-import {Chromatogram} from '..';
+import {fromJcamp} from '..';
 
@@ -13,5 +12,4 @@ const readFileAsync = Promise.promisify(fs.readFile);
     const jcamp = await readFileAsync(path, 'utf8');
-    const data = convert(jcamp, {newGCMS: true}).gcms;
-    const chrom = new Chromatogram(data);
+    const chrom = fromJcamp(jcamp);
     t.is(chrom.length, 6993);
 });

test/massFilter.js

@@ -46,5 +46,5 @@ import test from 'ava';
     let mass = [
-        [ [1, 2], [1, 1] ],
-        [ [1, 2, 5], [1, 1, 1] ],
-        [ [2, 4], [1, 1] ]
+        [[1, 2], [1, 1]],
+        [[1, 2, 5], [1, 1, 1]],
+        [[2, 4], [1, 1]]
     ];
@@ -65,3 +65,3 @@
     let peaks = [
-        { ms: {
+        {ms: {
             x: [1, 2, 3],
@@ -68,0 +68,0 @@ y: [1, 1, 1]

test/massInPeaks.js

@@ -6,3 +6,3 @@ import test from 'ava';
 import {join} from 'path';
-import {Chromatogram, massInPeaks, peakPicking} from '..';
+import {Chromatogram, massInPeaks, getPeaks} from '..';
 
@@ -23,3 +23,3 @@ const readFileAsync = Promise.promisify(fs.readFile);
 
-    let peakList = peakPicking(chrom);
+    let peakList = getPeaks(chrom);
     t.is(peakList.length, 312);
@@ -56,3 +56,3 @@
 
-    let peaks = peakPicking(chrom);
+    let peaks = getPeaks(chrom);
     t.is(peaks.length, 1);
@@ -73,5 +73,5 @@
     t.deepEqual(massInPeaks(peaks, [
-        [ [1, 2], [1, 1] ],
-        [ [1, 2, 5], [1, 1, 1] ],
-        [ [3, 4], [1, 1] ]
+        [[1, 2], [1, 1]],
+        [[1, 2, 5], [1, 1, 1]],
+        [[3, 4], [1, 1]]
     ]), [{
@@ -93,5 +93,5 @@ left: {index: 0},
     let mass = [
-        [ [1, 2], [1, 1] ],
-        [ [1, 2, 5], [1, 1, 1] ],
-        [ [2, 4], [1, 1] ]
+        [[1, 2], [1, 1]],
+        [[1, 2, 5], [1, 1, 1]],
+        [[2, 4], [1, 1]]
     ];
@@ -115,5 +115,5 @@
     let mass = [
-        [ [1, 2], [1, 1] ],
-        [ [1, 2, 5], [1, 1, 1] ],
-        [ [2, 4], [1, 2] ]
+        [[1, 2], [1, 1]],
+        [[1, 2, 5], [1, 1, 1]],
+        [[2, 4], [1, 2]]
     ];
@@ -120,0 +120,0 @@

test/scaleAlignment.js

@@ -54,9 +54,8 @@ import test from 'ava';
     let compared = spectraComparison(chrom1, chrom2, options);
-    t.deepEqual(compared.peaksSimilarity, [1, 1, 1, 1]);
-    t.deepEqual(compared.peaksFirst.map((val) => val.x), [20, 30, 40, 50]);
-    t.deepEqual(compared.peaksSecond.map((val) => val.x), [30, 40, 50, 60]);
+    t.deepEqual(compared.peaksSimilarity, [1, 1, 1, 1, 1]);
+    t.deepEqual(compared.peaksFirst.map((val) => val.x), [10, 20, 30, 40, 50]);
+    t.deepEqual(compared.peaksSecond.map((val) => val.x), [20, 30, 40, 50, 60]);
 
     let aligned = scaleAlignment(compared.peaksFirst, compared.peaksSecond);
-    t.deepEqual(aligned.reference.map((val) => val.x), [20, 30, 40, 50]);
-    t.deepEqual(aligned.sample.map((val) => val.x), [20, 30, 40, 50]);
+    t.is(Math.abs(aligned.scaleRegression.predict(30) - 20) < 1e-4, true);
 });
@@ -109,11 +108,10 @@
     let compared = spectraComparison(chrom1, chrom2, options);
-    t.deepEqual(compared.peaksSimilarity, [1, 1, 1, 1]);
-    t.deepEqual(compared.peaksFirst.map((val) => val.x), [20, 30, 40, 50]);
-    t.deepEqual(compared.peaksSecond.map((val) => val.x), [30, 40, 50, 60]);
+    t.deepEqual(compared.peaksSimilarity, [1, 1, 1, 1, 1]);
+    t.deepEqual(compared.peaksFirst.map((val) => val.x), [10, 20, 30, 40, 50]);
+    t.deepEqual(compared.peaksSecond.map((val) => val.x), [20, 30, 40, 50, 60]);
 
     let aligned = scaleAlignment(compared.peaksFirst, compared.peaksSecond, {computeQuality: true, stringFormula: 3});
-    t.deepEqual(aligned.reference.map((val) => val.x), [20, 30, 40, 50]);
-    t.deepEqual(aligned.sample.map((val) => val.x), [20, 30, 40, 50]);
-    t.is(aligned.stringFormula, 'y = 1.00*x-10.0');
-    t.is(aligned.r2, 1);
+    t.is(Math.abs(aligned.scaleRegression.predict(30) - 20) < 1e-4, true);
+    t.is(aligned.scaleRegression.toString(3), 'f(x) = 9.95e-17 * x^3 - 1.22e-14 * x^2 + 1.00 * x - 10.0');
+    t.is(Math.abs(aligned.r2 - 1) < 1e-4, true);
 });

test/spectraComparison.js

@@ -54,5 +54,5 @@ import test from 'ava';
     let compared = spectraComparison(chrom1, chrom2, options);
-    t.deepEqual(compared.peaksSimilarity, [1, 1, 1, 1]);
-    t.deepEqual(compared.peaksFirst.map((val) => val.x), [20, 30, 40, 50]);
-    t.deepEqual(compared.peaksSecond.map((val) => val.x), [30, 40, 50, 60]);
+    t.deepEqual(compared.peaksSimilarity, [1, 1, 1, 1, 1]);
+    t.deepEqual(compared.peaksFirst.map((val) => val.x), [10, 20, 30, 40, 50]);
+    t.deepEqual(compared.peaksSecond.map((val) => val.x), [20, 30, 40, 50, 60]);
 });
@@ -105,5 +105,5 @@
     let compared = spectraComparison(chrom1, chrom2, options);
-    t.deepEqual(compared.peaksSimilarity, [1, 1, 1]);
-    t.deepEqual(compared.peaksFirst.map((val) => val.x), [30, 40, 50]);
-    t.deepEqual(compared.peaksSecond.map((val) => val.x), [30, 40, 50]);
+    t.deepEqual(compared.peaksSimilarity, [1, 1, 1, 1]);
+    t.deepEqual(compared.peaksFirst.map((val) => val.x), [20, 30, 40, 50]);
+    t.deepEqual(compared.peaksSecond.map((val) => val.x), [20, 30, 40, 50]);
 });
@@ -126,3 +126,3 @@
         if (i < 45) {
-            ms2[i] = [[ 28, 29, 30, 31, 32, 56, 58, 60, 62, 64, 84, 87, 90, 93, 96 ], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]];
+            ms2[i] = [[28, 29, 30, 31, 32, 56, 58, 60, 62, 64, 84, 87, 90, 93, 96], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]];
         } else {
@@ -129,0 +129,0 @@ ms2[i] = [[i, 2 * i, 3 * i], [1, 1, 1]];

test/vectorify.js

@@ -6,3 +6,3 @@ import test from 'ava';
 import {join} from 'path';
-import {Chromatogram, massInPeaks, peakPicking, vectorify} from '..';
+import {Chromatogram, massInPeaks, getPeaks, vectorify} from '..';
 
@@ -23,3 +23,3 @@ const readFileAsync = Promise.promisify(fs.readFile);
 
-    let peakList = peakPicking(chrom);
+    let peakList = getPeaks(chrom);
     t.is(peakList.length, 312);
@@ -59,3 +59,3 @@
 
-    let peakList = peakPicking(chrom);
+    let peakList = getPeaks(chrom);
     t.is(peakList.length, 1);
@@ -74,3 +74,3 @@
     let peaks = [
-        { ms: {
+        {ms: {
             x: [1, 2, 3],
@@ -77,0 +77,0 @@ y: [1, 1, 1]

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

GitHub dependency

Supply chain risk

Contains a dependency which resolves to a GitHub URL. Dependencies fetched from GitHub specifiers are not immutable can be used to inject untrusted code or reduce the likelihood of a reproducible install.

Found 1 instance in 1 package

Manifest confusion

Supply chain risk

This package has inconsistent metadata. This could be malicious or caused by an error when publishing the package.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

26097981

increased by1.32%

Dev dependency count

7

decreased by-12.5%

Number of package files

66

increased by17.86%

Lines of code

22874

increased by9.05%

Number of lines in readme file

56

increased by36.59%

Number of high supply chain risk alerts

0

decreased by-100%

Number of medium supply chain risk alerts

14

decreased by-6.67%

Worsened metrics

Dependency count

4

increased by100%

Number of low supply chain risk alerts

7

increased by16.67%

Dependency changes

• + Addedbinary-search@^1.3.2

• + Addedjcampconverter@^2.3.0

• + Addedbinary-search@1.3.6(transitive)

• + Addedextend@3.0.2(transitive)

• + Addedjcampconverter@2.11.0(transitive)

• + Addedml-array-utils@0.3.0(transitive)

• + Addedml-curve-fitting@0.0.7(transitive)

• + Addedml-gsd@2.0.7(transitive)

• + Addedml-matrix@2.3.0(transitive)

• + Addedml-optimize-lorentzian@0.1.4(transitive)

• + Addedml-savitzky-golay-generalized@1.1.1(transitive)

• Updatedml-gsd@^2.0.1