alignment.js/app/FASTA/site_stacked_bar_chart.js

A suite of reusable [React](http://reactjs.org/) components for creating a variety of visualizations involving [multiple sequence alignments](https://en.wikipedia.org/wiki/Multiple_sequence_alignment). [View the live demo here](http://alignment.hyphy.org/

"use strict";

Object.defineProperty(exports, "__esModule", {
  value: true
});
exports["default"] = _default;

var _react = _interopRequireDefault(require("react"));

var _d = require("d3");

var _SiteStackedBarChart = _interopRequireDefault(require("../../SiteStackedBarChart.js"));

var _fasta = _interopRequireDefault(require("../../helpers/fasta"));

var _DataFetcher = _interopRequireDefault(require("../../components/DataFetcher.js"));

function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }

function _extends() { _extends = Object.assign || function (target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i]; for (var key in source) { if (Object.prototype.hasOwnProperty.call(source, key)) { target[key] = source[key]; } } } return target; }; return _extends.apply(this, arguments); }

function Spreader(props) {
  // Quick wrapper around DataFetcher for multiple props (potential feature)
  return /*#__PURE__*/_react["default"].createElement(_SiteStackedBarChart["default"], _extends({}, props.data, {
    label: "Nucleotide frequency"
  }));
}

function _default() {
  return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement("h1", null, "Site Stacked Bar Chart"), /*#__PURE__*/_react["default"].createElement(_DataFetcher["default"], {
    source: "data/CD2.fasta",
    modifier: function modifier(fasta) {
      var sequence_data = (0, _fasta["default"])(fasta),
          data = (0, _d.range)(sequence_data.number_of_sites).map(function (i) {
        var counts = sequence_data.map(function (record) {
          return record.seq[i];
        }).reduce(function (acc, curr) {
          acc[curr] += 1;
          return acc;
        }, {
          A: 0,
          C: 0,
          G: 0,
          T: 0,
          "-": 0
        }),
            total = counts["A"] + counts["C"] + counts["G"] + counts["T"];
        return [counts["A"] / total, counts["C"] / total, counts["G"] / total, counts["T"] / total];
      });
      return {
        sequence_data: sequence_data,
        data: data
      };
    }
  }, /*#__PURE__*/_react["default"].createElement(Spreader, null)));
}