Try the Materials Informatics Toolkit, which is designed to easily handle SMILES data. This and other helpful add-ins are available in the JMP® Marketplace
Created:
Mar 28, 2021 07:28 PM
| Last Modified: Jun 11, 2023 4:12 AM(1311 views)
I have a data set of patients of which I have created a composite index of critical illness. This composite includes patients who died, who had ventilator requirement, who had septic shock , required dialysis et cetera (about total 16 categories all nominal yes/no).
Reviewer want to know how much of these categories contributed to the composite. There are a total 600 patients who met the criteria of critical illness based on my definition.
I can provide information like the number of patients who died (n=xx), ventilator (n=yy).. All of them would be in the composite.
The sum of all these patients would be more than 600 because all of them are overlapping with the other.
Is there a way to solve this and maybe create a graph or diagram showing the overlap . I'm thinking of the bubble plot but there might be another way of doing this.
I'm not sure I fully understand your question so I am starting really simple, could you show number of unique patients with each condition? In this example every patient was tested for every condition so the total is the same, thus I would remove the 'does not apply' bars.
I would think the most immediate measure would be the total number of the 16 indicators that each patient had. To investigate the contribution of each indicator to the composite, Principal Component Analysis comes to mind (although there may be a better method with nominal variables, such as Multiple Correspondence Analysis).
I used predictor screening platform in JMP. With Composite index yes/no as Y variable and added all the variables as X.
It gave me ranking of all the variables as they contributed to the index along with their percentage contribution. This will work for my purpose, not 100% sure it is the right way though as the variables are components of the composite
'
var data = div.getElementsByClassName("video-js");
var script = document.createElement('script');
script.src = "https://players.brightcove.net/" + data_account + "/" + data_palyer + "_default/index.min.js";
for(var i=0;i< data.length;i++){
videodata.push(data[i]);
}
}
}
for(var i=0;i< videodata.length;i++){
document.getElementsByClassName('lia-vid-container')[i].innerHTML = videodata[i].outerHTML;
document.body.appendChild(script);
}
}
catch(e){
}
/* Re compile html */
$compile(rootElement.querySelectorAll('div.lia-message-body-content')[0])($scope);
}
if (code_l.toLowerCase() != newBody.getAttribute("slang").toLowerCase()) {
/* Adding Translation flag */
var tr_obj = $filter('filter')($scope.sourceLangList, function (obj_l) {
return obj_l.code.toLowerCase() === newBody.getAttribute("slang").toLowerCase()
});
if (tr_obj.length > 0) {
tr_text = "This post originally written in lilicon-trans-text has been computer translated for you. When you reply, it will also be translated back to lilicon-trans-text.".replace(/lilicon-trans-text/g, tr_obj[0].title);
try {
if ($scope.wootMessages[$rootScope.profLang] != undefined) {
tr_text = $scope.wootMessages[$rootScope.profLang].replace(/lilicon-trans-text/g, tr_obj[0].title);
}
} catch (e) {
}
} else {
//tr_text = "This message was translated for your convenience!";
tr_text = "This message was translated for your convenience!";
}
try {
if (!document.getElementById("tr-msz-" + value)) {
var tr_para = document.createElement("P");
tr_para.setAttribute("id", "tr-msz-" + value);
tr_para.setAttribute("class", "tr-msz");
tr_para.style.textAlign = 'justify';
var tr_fTag = document.createElement("IMG");
tr_fTag.setAttribute("class", "tFlag");
tr_fTag.setAttribute("src", "/html/assets/lingoTrFlag.PNG");
tr_fTag.style.marginRight = "5px";
tr_fTag.style.height = "14px";
tr_para.appendChild(tr_fTag);
var tr_textNode = document.createTextNode(tr_text);
tr_para.appendChild(tr_textNode);
/* Woot message only for multi source */
if(rootElement.querySelector(".lia-quilt-forum-message")){
rootElement.querySelector(".lia-quilt-forum-message").appendChild(tr_para);
} else if(rootElement.querySelector(".lia-message-view-blog-topic-message")) {
rootElement.querySelector(".lia-message-view-blog-topic-message").appendChild(tr_para);
} else if(rootElement.querySelector(".lia-quilt-blog-reply-message")){
rootElement.querySelector(".lia-quilt-blog-reply-message").appendChild(tr_para);
} else if(rootElement.querySelector(".lia-quilt-tkb-message")){
rootElement.querySelector(".lia-quilt-tkb-message").appendChild(tr_para);
} else if(rootElement.querySelector(".lia-quilt-tkb-reply-message")){
rootElement.querySelector(".lia-quilt-tkb-reply-message").insertBefore(tr_para,rootElement.querySelector(".lia-quilt-row.lia-quilt-row-footer"));
} else if(rootElement.querySelector(".lia-quilt-idea-message")){
rootElement.querySelector(".lia-quilt-idea-message").appendChild(tr_para);
}else if(rootElement.querySelector(".lia-quilt-column-alley-left")){
rootElement.querySelector(".lia-quilt-column-alley-left").appendChild(tr_para);
}
else {
if (rootElement.querySelectorAll('div.lia-quilt-row-footer').length > 0) {
rootElement.querySelectorAll('div.lia-quilt-row-footer')[0].appendChild(tr_para);
} else {
rootElement.querySelectorAll('div.lia-quilt-column-message-footer')[0].appendChild(tr_para);
}
}
}
} catch (e) {
}
}
} else {
/* Do not display button for same language */
// syncList.remove(value);
var index = $scope.syncList.indexOf(value);
if (index > -1) {
$scope.syncList.splice(index, 1);
}
}
}
}
}
}
angular.forEach(mszList_l, function (value) {
if (document.querySelectorAll('div.lia-js-data-messageUid-' + value).length > 0) {
var rootElements = document.querySelectorAll('div.lia-js-data-messageUid-' + value);
}else if(document.querySelectorAll('.lia-occasion-message-view .lia-component-occasion-message-view').length >0){
var rootElements = document.querySelectorAll('.lia-occasion-message-view .lia-component-occasion-message-view')[0].querySelectorAll('.lia-occasion-description')[0];
}else {
var rootElements = document.querySelectorAll('div.message-uid-' + value);
}
angular.forEach(rootElements, function (rootElement) {
if (value == '372120' && "ForumTopicPage" == "TkbArticlePage") {
rootElement = document.querySelector('.lia-thread-topic');
}
/* V1.1 Remove from UI */
if (document.getElementById("tr-msz-" + value)) {
document.getElementById("tr-msz-" + value).remove();
}
if (document.getElementById("tr-sync-" + value)) {
document.getElementById("tr-sync-" + value).remove();
}
/* XPath expression for subject and Body */
var lingoRBExp = "//lingo-body[@id = " + "'lingo-body-" + value + "'" + "]";
lingoRSExp = "//lingo-sub[@id = " + "'lingo-sub-" + value + "'" + "]";
/* Get translated subject of the message */
lingoRSXML = doc.evaluate(lingoRSExp, doc, null, XPathResult.UNORDERED_NODE_SNAPSHOT_TYPE, null);
for (var i = 0; i < lingoRSXML.snapshotLength; i++) {
/* Replace Reply/Comment subject with transalted subject */
var newSub = lingoRSXML.snapshotItem(i);
/*** START : extracting subject from source if selected language and source language is same **/
var sub_L = "";
if (newSub.getAttribute("slang").toLowerCase() == code_l.toLowerCase()) {
if (value == '372120') {
sub_L = decodeURIComponent($scope.sourceContent[value].subject);
}
else{
sub_L = decodeURIComponent($scope.sourceContent[value].subject);
}
} else {
sub_L = newSub.innerHTML;
}
/*** End : extracting subject from source if selected language and source language is same **/
/* This code is placed to remove the extra meta tag adding in the UI*/
try{
sub_L = sub_L.replace('<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />','');
}
catch(e){
}
// if($scope.viewTrContentOnly || (newSub.getAttribute("slang").toLowerCase() != code_l.toLowerCase())) {
if ($scope.viewTrContentOnly) {
if ("ForumTopicPage" == "IdeaPage") {
if (value == '372120') {
if( (sub_L != "") && (sub_L != undefined) && (sub_L != "undefined") ){
document.querySelector('.MessageSubject .lia-message-subject').innerHTML = sub_L;
}
}
}
if ("ForumTopicPage" == "TkbArticlePage") {
if (value == '372120') {
if( (sub_L != "") && (sub_L != undefined) && (sub_L != "undefined") ){
var subTkbElement = document.querySelector('.lia-thread-subject');
if(subTkbElement){
document.querySelector('.lia-thread-subject').innerHTML = sub_L;
}
}
}
}
else if ("ForumTopicPage" == "BlogArticlePage") {
if (value == '372120') {
try {
if((sub_L != "") && (sub_L!= undefined) && (sub_L != "undefined")){
var subElement = rootElement.querySelector('.lia-blog-article-page-article-subject');
if(subElement) {
subElement.innerText = sub_L;
}
}
} catch (e) {
}
/* var subElement = rootElement.querySelectorAll('.lia-blog-article-page-article-subject');
for (var subI = 0; subI < subElement.length; subI++) {
if((sub_L != "") && (sub_L!= undefined) && (sub_L != "undefined")){
subElement[subI].innerHTML = sub_L;
}
} */
}
else {
try {
// rootElement.querySelectorAll('.lia-blog-article-page-article-subject').innerHTML= sub_L;
/** var subElement = rootElement.querySelectorAll('.lia-blog-article-page-article-subject');
for (var j = 0; j < subElement.length; j++) {
if( (sub_L != "") && (sub_L != undefined) && (sub_L != "undefined") ){
subElement[j].innerHTML = sub_L;
}
} **/
} catch (e) {
}
}
}
else {
if (value == '372120') {
try{
/* Start: This code is written by iTalent as part of iTrack LILICON - 98 */
if( (sub_L != "") && (sub_L != undefined) && (sub_L != "undefined") ){
if(document.querySelectorAll('.lia-quilt-forum-topic-page').length > 0){
if(rootElement.querySelector('div.lia-message-subject').querySelector('h5')){
rootElement.querySelector('div.lia-message-subject').querySelector('h5').innerText = decodeURIComponent(sub_L);
} else {
rootElement.querySelector('.MessageSubject .lia-message-subject').innerText = sub_L;
}
} else {
rootElement.querySelector('.MessageSubject .lia-message-subject').innerText = sub_L;
}
}
/* End: This code is written by iTalent as part of iTrack LILICON - 98 */
}
catch(e){
console.log("subject not available for second time. error details: " + e);
}
} else {
try {
/* Start: This code is written by iTalent as part of LILICON - 98 reported by Ian */
if ("ForumTopicPage" == "IdeaPage") {
if( (sub_L != "") && (sub_L != undefined) && (sub_L != "undefined") ){
document.querySelector('.lia-js-data-messageUid-'+ value).querySelector('.MessageSubject .lia-message-subject').innerText = sub_L;
}
}
else{
if( (sub_L != "") && (sub_L != undefined) && (sub_L != "undefined") ){
rootElement.querySelector('.MessageSubject .lia-message-subject').innerText = sub_L;
/* End: This code is written as part of LILICON - 98 reported by Ian */
}
}
} catch (e) {
console.log("Reply subject not available. error details: " + e);
}
}
}
// Label translation
var labelEle = document.querySelector("#labelsForMessage");
if (!labelEle) {
labelEle = document.querySelector(".LabelsList");
}
if (labelEle) {
var listContains = labelEle.querySelector('.label');
if (listContains) {
/* Commenting this code as bussiness want to point search with source language label */
// var tagHLink = labelEle.querySelectorAll(".label")[0].querySelector(".label-link").href.split("label-name")[0];
var lingoLabelExp = "//lingo-label/text()";
trLabels = [];
trLabelsHtml = "";
/* Get translated labels of the message */
lingoLXML = doc.evaluate(lingoLabelExp, doc, null, XPathResult.UNORDERED_NODE_SNAPSHOT_TYPE, null);
/* try{
for(var j=0;j,';
}
trLabelsHtml = trLabelsHtml+'