peaks-similarity/README.md

Peaks similarity - calculate the similarity between 2 ordered arrays of peaks

# peaks-similarity

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[![build status][travis-image]][travis-url]
[![David deps][david-image]][david-url]
[![npm download][download-image]][download-url]

Peaks similarity - calculate a similarity between 0 and 1 of 2 arrays of [x,y] points.

## Description

The idea is to calculate a similarity value between 0 and 1 between two arrays of peaks ([x,y] points).

```javascript
const peaks1 = [
  [1, 1],
  [2, 2],
];
const peaks2 = [
  [1, 2],
  [2, 1],
];

import Comparator from 'peaks-similarity';
const comparator = new Comparator({ widthBottom: 4, widthTop: 2 });
const result = comparator.getSimilarity(peaks1, peaks2);

console.log(result);
```

options

- widthBottom : bottom width of the trapezoid (default: 2)
- widthTop : top width of the trapezoid (default: 1)
- trapezoid : Should we use overlapping of trapezoids surface (default: false). If trapezoid is false it is based only on peaks and not surface.
- common: Only take the common part of the array based on the widthBottom of the trapezoid (default: false)
  - true: take the common part between the 2 array
  - first: keep first array and take the common part of the second one
  - second: keep second array and take the common part of the first one

## Methods

- setOptions(newOptions)
- setPeaks1(anArray)
- setPeaks2(anArray)
- getExtract1()
- getExtract2()
- getExtractInfo1()
- getExtractInfo2()
- setTrapezoid(newWidthBottom, newWidthTop)
- setFromTo(newFrom, newTo)
- getOverlap(x1, y1, x2, y2)
- getOverlapTrapezoid(x1, y1, x2, y2)
- calculateDiff()
- checkArray(points)
- getSimilarity(newPeaks1, newPeaks2)
- fastSimilarity(newPeaks2, from, to)
  - newPeaks2 has to be normalized (sum to 1)
  - fastSimilarity will use the common parameter. This parameter
    may be 'second' and will take the peaks1 that are at a distance less
    than widthBottom of any peak of peaks2

## License

[MIT](./LICENSE)

[npm-image]: https://img.shields.io/npm/v/peaks-similarity.svg
[npm-url]: https://www.npmjs.com/package/peaks-similarity
[ci-image]: https://github.com/cheminfo/peaks-similarity/workflows/Node.js%20CI/badge.svg?branch=main
[ci-url]: https://github.com/cheminfo/peaks-similarity/actions?query=workflow%3A%22Node.js+CI%22
[codecov-image]: https://img.shields.io/codecov/c/github/cheminfo/peaks-similarity.svg
[codecov-url]: https://codecov.io/gh/cheminfo/peaks-similarity
[download-image]: https://img.shields.io/npm/dm/peaks-similarity.svg
[download-url]: https://www.npmjs.com/package/peaks-similarity