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刘莉莉 实现empirical p value #20

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刘莉莉 实现empirical p value #20

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74630dc
更新新的js文件名称
BaekLi May 22, 2020
b8dd371
上传empirical_pvalue.js文件
BaekLi May 22, 2020
552d420
在main.js里面添加使用empirical_pvalue.js的语句，并将结果添加在表格中
BaekLi May 22, 2020
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2 changes: 1 addition & 1 deletion gene_expression_scatter_plot/gene_scatter_plot_home.html
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Expand Up @@ -14,7 +14,7 @@
<script src="js/tableExport.js"></script>
<script src="js/jquery.base64.js"></script>
<!-- 刘莉莉添加epvalue.js -->
<script src="js/epvalue.js"></script>
<script src="js/empirical_pvalue.js"></script>
<link rel="stylesheet" href="css/animate.min.css">
<link rel="stylesheet" href="css/jquery.gDialog.css">
<script src="js/jquery.gDialog.js"></script>
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74 changes: 74 additions & 0 deletions gene_expression_scatter_plot/js/empirical_pvalue.js
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@@ -0,0 +1,74 @@
// JavaScript Document
/*
计算 Empirical P-Value,无返回值,计算得到的Empirical P-Value均存储到传过来的数组中,groups与totals.
变量gene1,gene2表示json格式的G1,G2数据数组;
变量datas是main.js里的,存储每个tissue下的坐标;
变量groups是main.js里的,存储每个datas的tissue，相关系数，个数，pvalue信息;
变量totals是main.js里的,记录所有点数的pvalue，Empirical P-Value.
*/
function empirical_p(gene1,gene2,datas,groups,totals){
// count数组用来统计随机排列后每组数据的相关系数大于原排列后的个数
var count = new Array(groups.length+1).fill(0);
// total随机排列后所有点数的pvalue与Empirical P-Value,对应totals
var total = new Array();
// console.log(totals);
// 重复10000次
var round = 10000;
console.log("计算 10000 次");
for(var m = 0;m<round ;m++){
// 随机排列后的data与group,对应datas与groups
var data = new Array();
var group = new Array();
// 得到新的gene1/gene2随机排列后的数组
var newGene1 = randomJson(gene1);
var newGene2 = randomJson(gene2);
// console.log(newGene1);
// num用来遍历点,不断累加,直到最后一个点
var num = 0;
// 计算随机排序后的data
for(var i=0;i<datas.length;i++){
// 用数组记录随机排序后每个tissue里所有点的坐标
data[i] = new Array();
// 遍历坐标值,生成随机排序后每个点的新坐标
for(var j=0;j<datas[i].length;j = j+2){
data[i].push(newGene1[num]);
data[i].push(newGene2[num]);
num++;
}
}
// 使用main.js里的getCorrelationCoefficientAndSetGroups函数,填充group与total数组,获得相关系数
getCorrelationCoefficientAndSetGroups (data,group,total);
// 遍历计算随机排列后每组数据的相关系数大于原排列后的个数
for(var k=0;k<count.length-1;k++){
// 比较的相关系数是绝对值
if(group[k][1]>groups[k][1]){
count[k]++;
}
//比较的是非绝对值的相关系数 k<count.length
// if(total[k]>totals[k]){
// count[k]++;
// }
}
// m是随机循环的参数;在每次循环都比较一下随机排序和原顺序的所有点的相关系数
if(total[m]>totals[0]){
count[groups.length]++;
}
}
// 计算每个tissue的Empirical P-Value,并放在传参的groups里
for(var i=0;i<groups.length;i++){
count[i]=count[i]/round;
groups[i].push(count[i]);
}
// 计算所有点的Empirical P-Value,并放在传参的totals里
totals.push(count[groups.length]/round);
}
// 随机排列数组内的数据
function randomJson(arr){
for (let i = 1; i < arr.length; i++) {
// 产生有效随机数
const random = Math.floor(Math.random() * (i + 1));
// 随机交换数组元素数据
[arr[i], arr[random]] = [arr[random], arr[i]];
}
return arr;
}
71 changes: 51 additions & 20 deletions gene_expression_scatter_plot/js/main.js
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Original file line number Diff line number Diff line change
Expand Up @@ -100,8 +100,15 @@ function condition_specific_correlation(g1, g2, info){
if(a){
//使用json文件内容计算并赋值给tissues, datas, details,gene1,gene2等全局变量，返回值为可绘制种类的数量
var numberOfExecuted = makeJsonIntoArray(G1, G2, INFO, a);
//表格排序
lastLineCorrelationCoefficient = getCorrelationCoefficientAndSetGroups();
//表格排序，传入参数
lastLineCorrelationCoefficient = getCorrelationCoefficientAndSetGroups(datas,groups,totals);
//计算运行时间
console.time("empirical_p");
// 计算Empirical P-Value
empirical_p(gene1,gene2,datas,groups,totals);
console.timeEnd("empirical_p");
// 表格最后一行
lastLineCorrelationCoefficient = "<tr>" + lastLineCorrelationCoefficient + "<td><b>" + totals[1].toFixed(4)+ "<b></td></tr>"
if (numberOfExecuted != 0) {
// 以第二排的相关系数进行排序
sortByColumn(2);
Expand Down Expand Up @@ -299,6 +306,7 @@ function setAndDisplayUtilization (numberOfExecuted, numberOfExecutedInfor, numb
numberOfExecutedInfor + "/" + numberOfInformation;
}
}
// 根据column进行排序
function sortByColumn(numForChangingTheOrderByColumn) {
var str = "";
for (var i = 0; i < groups.length - 1; i++) {
Expand All @@ -309,74 +317,93 @@ function sortByColumn(numForChangingTheOrderByColumn) {
var temp3 = groups[i][2];
var temp4 = groups[i][3];
var temp5 = groups[i][4];
// 给表格添加新的数据，Empirical P-Value
var temp6 = groups[i][5];
groups[i][0] = groups[j][0];
groups[i][1] = groups[j][1];
groups[i][2] = groups[j][2];
groups[i][3] = groups[j][3];
groups[i][4] = groups[j][4];
groups[i][5] = groups[j][5];
groups[j][0] = temp1;
groups[j][1] = temp2;
groups[j][2] = temp3;
groups[j][3] = temp4;
groups[j][4] = temp5;
groups[j][5] = temp6;
}
}
}
//根据选择的列进行排序
switch (numForChangingTheOrderByColumn) {
case 1:
if (numForChangingTheOrderByTissue % 2 == 0) {
for (var i = 0; i < groups.length; i++) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td></tr>";
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
else {
for (var i = groups.length - 1; i >= 0; i--) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td></tr>";
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
numForChangingTheOrderByTissue++;
break;
case 2:
if (numForChangingTheOrderByCoefficient % 2 == 0) {
for (var i = 0; i < groups.length; i++) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td></tr>";
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
else {
for (var i = groups.length - 1; i >= 0; i--) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td></tr>";
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
numForChangingTheOrderByCoefficient++;
break;
case 3:
if (numForChangingTheOrderByNumber % 2 == 0) {
for (var i = 0; i < groups.length; i++) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td></tr>";
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
else {
for (var i = groups.length - 1; i >= 0; i--) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td></tr>";
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
numForChangingTheOrderByNumber++;
break;
case 4:
if (numForChangingTheOrderByP % 2 == 0) {
for (var i = 0; i < groups.length; i++) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td></tr>";
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
else {
for (var i = groups.length - 1; i >= 0; i--) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td></tr>";
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
numForChangingTheOrderByP++;
break;
case 6:
if (numForChangingTheOrderByEP % 2 == 0) {
for (var i = 0; i < groups.length; i++) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
else {
for (var i = groups.length - 1; i >= 0; i--) {
str = str + "<tr><td>" + groups[i][0] + "</td><td>" + groups[i][1].toFixed(5) + groups[i][4] + "</td><td>" + groups[i][2] + "</td><td>" + makeNumberToStringAndExponential(groups[i][3]) + "</td><td>" +groups[i][5].toFixed(4) + "</td></tr>";
}
}
numForChangingTheOrderByEP++;
break;
}
str = "<tr><th><p onclick='sortByColumn(1);'>" + strTissueSettings + "</p></th><th><p onclick='sortByColumn(2);'>Correlation Coefficient</p></th><th><p onclick='sortByColumn(3);'>Number</p></th><th style='width: 200px;'><p onclick='sortByColumn(4);'>P Value (one-tail)</p></th></tr>" +
// 点击相应的column就可以进行该column的排序
str = "<tr><th><p onclick='sortByColumn(1);'>" + strTissueSettings + "</p></th><th><p onclick='sortByColumn(2);'>Correlation Coefficient</p></th><th><p onclick='sortByColumn(3);'>Number</p></th><th style='width: 200px;'><p onclick='sortByColumn(4);'>P Value (one-tail)</p></th><th><p onclick='sortByColumn(6);'>Empirical P-Value</p></th></tr>" +
str + lastLineCorrelationCoefficient;
document.getElementById("id_main_output_table").innerHTML = str;
}
Expand Down Expand Up @@ -659,7 +686,8 @@ function isExistInDetailMatchs(detail) {
}
return false;
}
function getCorrelationCoefficientAndSetGroups () {
// 计算相关系数并为groups赋值，并用形参来代替全局变量
function getCorrelationCoefficientAndSetGroups (data,group,total) {
var tail = 1;
var str = "";
var correlationCoefficient1 = 0;
Expand All @@ -672,7 +700,7 @@ function getCorrelationCoefficientAndSetGroups () {
var squareOfAverageY1 = 0;
var averageXTimesAverageY1 = 0;
var allN = 0;
for (var i = 0; i < datas.length; i++) {
for (var i = 0; i < data.length; i++) {
var correlationCoefficient = 0;
var sumOfSquareOfX = 0;
var sumOfSquareOfY = 0;
Expand All @@ -682,9 +710,9 @@ function getCorrelationCoefficientAndSetGroups () {
var squareOfAverageX = 0;
var squareOfAverageY = 0;
var averageXTimesAverageY = 0;
for (var j = 0; j < datas[i].length; j = j + 2) {
var x = datas[i][j];
var y = datas[i][j + 1];
for (var j = 0; j < data[i].length; j = j + 2) {
var x = data[i][j];
var y = data[i][j + 1];
sumOfSquareOfX += x * x;
sumOfSquareOfY += y * y;
sumOfXTimesY += x * y;
Expand All @@ -697,7 +725,8 @@ function getCorrelationCoefficientAndSetGroups () {
averageY1 += y;
allN++;
}
var doN = datas[i].length / 2;
// doN为同个issue的点的个数
var doN = data[i].length / 2;
averageX /= doN;
averageY /= doN;
squareOfAverageX = averageX * averageX;
Expand All @@ -713,7 +742,8 @@ function getCorrelationCoefficientAndSetGroups () {
sign = " (NaN)";
}
var pValue = correlationCoefficientToPValue(correlationCoefficient, doN, 1);
groups[i] = new Array(tissues[i], Math.abs(correlationCoefficient), doN, pValue, sign);
//total.push(correlationCoefficient); //如果比较非绝对值的相关系数
group[i] = new Array(tissues[i], Math.abs(correlationCoefficient), doN, pValue, sign);
}
averageX1 /= allN;
averageY1 /= allN;
Expand All @@ -729,8 +759,9 @@ function getCorrelationCoefficientAndSetGroups () {
correlationCoefficient1 = 0;
sign = " (NaN)";
}
var pTemp = correlationCoefficientToPValue(correlationCoefficient1, allN, 1);
return "<tr><td><b>total</b></td><td><b>" + correlationCoefficient1.toFixed(5) + sign + "</b></td><td><b>" + allN + "</b></td><td><b>" + makeNumberToStringAndExponential(pTemp) + "<b></td></tr>";
var totalPTemp = correlationCoefficientToPValue(correlationCoefficient1, allN, 1);
total.push(correlationCoefficient1);
return "<td><b>total</b></td><td><b>" + correlationCoefficient1.toFixed(5) + sign + "</b></td><td><b>" + allN + "</b></td><td><b>" + makeNumberToStringAndExponential(totalPTemp) + "<b></td>";
}
function getTissues() {
return this.tissues;
Expand Down