layout-base/src/util/Matrix.js

Basic layout model and some utilities for Cytoscape.js layout extensions

// Some matrix (1d and 2d array) operations
function Matrix() {
}

/**
 * matrix multiplication
 * array1, array2 and result are 2d arrays
 */
Matrix.multMat = function(array1, array2){
  let result = [];

  for(let i = 0; i < array1.length; i++){
      result[i] = [];
      for(let j = 0; j < array2[0].length; j++){
        result[i][j] = 0;
        for(let k = 0; k < array1[0].length; k++){
          result[i][j] += array1[i][k] * array2[k][j]; 
        }
      }
    } 
  return result;
};

/**
 * matrix transpose
 * array and result are 2d arrays
 */
Matrix.transpose = function(array){
  let result = [];
  
  for(let i = 0; i < array[0].length; i++){
    result[i] = [];
    for(let j = 0; j < array.length; j++){
      result[i][j] = array[j][i];
    }
  }
  
  return result;
};

/**
 * multiply array with constant
 * array and result are 1d arrays
 */
Matrix.multCons = function(array, constant){
  let result = [];

  for(let i = 0; i < array.length; i++){
    result[i] = array[i] * constant;
  }

  return result;
};

/**
 * substract two arrays
 * array1, array2 and result are 1d arrays
 */
Matrix.minusOp = function(array1, array2){
  let result = [];

  for(let i = 0; i < array1.length; i++){
    result[i] = array1[i] - array2[i];
  }

  return result;
};

/**
 * dot product of two arrays with same size
 * array1 and array2 are 1d arrays
 */
Matrix.dotProduct = function(array1, array2){
  let product = 0;

  for(let i = 0; i < array1.length; i++){
    product += array1[i] * array2[i]; 
  }

  return product;
};

/**
 * magnitude of an array
 * array is 1d array
 */
Matrix.mag = function(array){
  return Math.sqrt(this.dotProduct(array, array));
};

/**
 * normalization of an array
 * array and result are 1d array
 */
Matrix.normalize = function(array){
  let result = [];
  let magnitude = this.mag(array);

  for(let i = 0; i < array.length; i++){
    result[i] = array[i] / magnitude;
  }

  return result;
};

/**
 * multiply an array with centering matrix
 * array and result are 1d array
 */
Matrix.multGamma = function(array){
  let result = [];
  let sum = 0;

  for(let i = 0; i < array.length; i++){
    sum += array[i];
  }

  sum *= (-1)/array.length;

  for(let i = 0; i < array.length; i++){
    result[i] = sum + array[i];
  }     
  return result;
};

/**
 * a special matrix multiplication
 * result = 0.5 * C * INV * C^T * array
 * array and result are 1d, C and INV are 2d arrays
 */
Matrix.multL = function(array, C, INV){
  let result = [];
  let temp1 = [];
  let temp2 = [];

  // multiply by C^T
  for(let i = 0; i < C[0].length; i++){
    let sum = 0;
    for(let j = 0; j < C.length; j++){
      sum += -0.5 * C[j][i] * array[j]; 
    }
    temp1[i] = sum;
  }
  // multiply the result by INV
  for(let i = 0; i < INV.length; i++){
    let sum = 0;
    for(let j = 0; j < INV.length; j++){
      sum += INV[i][j] * temp1[j]; 
    }
    temp2[i] = sum;
  }  
  // multiply the result by C
  for(let i = 0; i < C.length; i++){
    let sum = 0;
    for(let j = 0; j < C[0].length; j++){
      sum += C[i][j] * temp2[j]; 
    }
    result[i] = sum;
  } 

  return result;
};

module.exports = Matrix;