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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.9.38">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<meta name="author" content="v1.2.1">
<meta name="description" content="EXAM (ex-vivo allograft monitoring) is an analytics dashboard for the hypothermic machine perfusion data in deceased-donor kidney transplantation.">
<title>EXAM</title>
<style>
/* Default styles provided by pandoc.
** See https://pandoc.org/MANUAL.html#variables-for-html for config info.
*/
code{white-space: pre-wrap;}
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div.columns{display: flex; gap: min(4vw, 1.5em);}
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ul.task-list{list-style: none;}
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width: 0.8em;
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vertical-align: middle;
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<link href="exam-app_files/libs/quarto-html/tippy.css" rel="stylesheet">
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<script src="exam-app_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="exam-app_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
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<script src="exam-app_files/libs/quarto-dashboard/quarto-dashboard.js"></script>
<script src="exam-app_files/libs/quarto-dashboard/stickythead.js"></script>
<script src="exam-app_files/libs/quarto-dashboard/web-components.js" type="module"></script>
<script src="exam-app_files/libs/quarto-dashboard/components.js"></script>
<!-- favicon -->
<link rel="icon" type="image/png" href="./images/Kreis_Niere_196x196.png">
<!-- Plausible -->
<script async="" src="https://plausible.io/js/pa-iA2W4aMrjS4HpLwVcKA1O.js"></script>
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window.plausible=window.plausible||function(){(plausible.q=plausible.q||[]).push(arguments)},plausible.init=plausible.init||function(i){plausible.o=i||{}};
plausible.init()
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#dashboard-collapse" aria-controls="dashboard-collapse" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="navbar-brand-container">
<a href="#"><img src="images/SWT_2955_2021_border.png" alt="" class="navbar-logo light-content d-inline-block"></a>
<a href="#"><img src="images/SWT_2955_2021_border.png" alt="" class="navbar-logo dark-content d-inline-block"></a>
<div class="navbar-title">
<div class="navbar-title-text"><a href="#">EXAM</a></div>
<div class="navbar-author">v1.2.1</div>
</div>
</div>
<div id="dashboard-collapse" class="navbar-collapse collapse"><ul class="navbar-nav navbar-nav-scroll me-auto" role="tablist"><li class="nav-item" role="presentation"><a id="tab-kidney-lifeport-dashboard" class="nav-link active" data-bs-toggle="tab" role="tab" data-bs-target="#kidney-lifeport-dashboard" data-scrolling="false" href="#kidney-lifeport-dashboard" aria-controls="kidney-lifeport-dashboard" aria-selected="true"><span class="nav-link-text">Kidney LifePort Dashboard</span></a></li><li class="nav-item" role="presentation"><a id="tab-indicators" class="nav-link" data-bs-toggle="tab" role="tab" data-bs-target="#indicators" data-scrolling="false" href="#indicators" aria-controls="indicators" aria-selected="false"><span class="nav-link-text">Indicators</span></a></li><li class="nav-item" role="presentation"><a id="tab-about" class="nav-link" data-bs-toggle="tab" role="tab" data-bs-target="#about" data-scrolling="false" href="#about" aria-controls="about" aria-selected="false"><span class="nav-link-text">About</span></a></li></ul><div class="quarto-dashboard-links"><a class="quarto-dashboard-link" href="https://github.com/Swisstransplant/EXAM"><i class="bi bi-github"></i></a></div></div></div>
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<div class="page-layout-custom quarto-dashboard-content bslib-gap-spacing html-fill-container bslib-page-fill quarto-dashboard-pages dashboard-sidebar-container">
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<div class="tab-content bslib-grid html-fill-item html-fill-container" style="display: grid; grid-template-columns: minmax(3em, 1fr);
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<div id="kidney-lifeport-dashboard" class="dashboard-page tab-pane show active html-fill-item html-fill-container" data-orientation="rows" aria-labelledby="tab-kidney-lifeport-dashboard">
<div class="html-fill-item html-fill-container bslib-grid" style="display: grid; grid-template-rows: minmax(3em, 13fr) minmax(3em, 37fr) minmax(3em, 37fr) minmax(3em, 13fr); grid-auto-columns: minmax(0, 1fr);">
<div class="html-fill-item html-fill-container bslib-grid" style="display: grid; grid-template-columns: minmax(3em, 1fr);
grid-auto-rows: minmax(0, 1fr);">
<div class="card cell html-fill-item html-fill-container bslib-card" data-title="Organ and Device Information" data-bslib-card-init="" data-require-bs-caller="card()" data-full-screen="false">
<div class="card-header"><div class="card-title html-fill-item html-fill-container"><span style="display: inline">
Organ and Device Information
</span></div></div>
<div class="card-body html-fill-item html-fill-container">
<div class="cell-output-display html-fill-item html-fill-container no-overflow-x">
<div id="Tab_info" class="shiny-html-output shiny-table-output html-fill-item html-fill-container"></div>
</div>
</div>
<bslib-tooltip placement="auto" bsoptions="[]" data-require-bs-version="5" data-require-bs-caller="tooltip()">
<template>Expand</template>
<span class="bslib-full-screen-enter badge rounded-pill">
<svg xmlns="http://www.w3.org/2000/svg" viewbox="0 0 24 24" style="height:1em;width:1em;" aria-hidden="true" role="img"><path d="M20 5C20 4.4 19.6 4 19 4H13C12.4 4 12 3.6 12 3C12 2.4 12.4 2 13 2H21C21.6 2 22 2.4 22 3V11C22 11.6 21.6 12 21 12C20.4 12 20 11.6 20 11V5ZM4 19C4 19.6 4.4 20 5 20H11C11.6 20 12 20.4 12 21C12 21.6 11.6 22 11 22H3C2.4 22 2 21.6 2 21V13C2 12.4 2.4 12 3 12C3.6 12 4 12.4 4 13V19Z"></path></svg>
</span>
</bslib-tooltip><script data-bslib-card-init="">bslib.Card.initializeAllCards();</script></div>
</div>
<div class="flow bslib-grid" data-layout="flow" style="display: grid; grid-template-columns: minmax(3em, 1fr) minmax(3em, 1fr);
grid-auto-rows: minmax(0, 1fr);">
<div class="card html-fill-item html-fill-container bslib-card" data-title="Pressure" data-bslib-card-init="" data-require-bs-caller="card()" data-full-screen="false">
<div class="card-header"><div class="card-title html-fill-item html-fill-container"><span style="display: inline">
Pressure
</span></div></div>
<div class="cell card-body html-fill-item html-fill-container" style="padding: 16px;">
<div class="cell-output-display html-fill-item html-fill-container">
<div class="plotly html-widget html-widget-output shiny-report-size shiny-report-theme html-fill-item html-fill-container" id="Fig1" style="width:100%;height:300px;"></div>
</div>
<div class="cell-output-display html-fill-item html-fill-container no-overflow-x">
<div id="Tab1" class="shiny-html-output shiny-table-output html-fill-item html-fill-container"></div>
</div>
</div>
<bslib-tooltip placement="auto" bsoptions="[]" data-require-bs-version="5" data-require-bs-caller="tooltip()">
<template>Expand</template>
<span class="bslib-full-screen-enter badge rounded-pill">
<svg xmlns="http://www.w3.org/2000/svg" viewbox="0 0 24 24" style="height:1em;width:1em;" aria-hidden="true" role="img"><path d="M20 5C20 4.4 19.6 4 19 4H13C12.4 4 12 3.6 12 3C12 2.4 12.4 2 13 2H21C21.6 2 22 2.4 22 3V11C22 11.6 21.6 12 21 12C20.4 12 20 11.6 20 11V5ZM4 19C4 19.6 4.4 20 5 20H11C11.6 20 12 20.4 12 21C12 21.6 11.6 22 11 22H3C2.4 22 2 21.6 2 21V13C2 12.4 2.4 12 3 12C3.6 12 4 12.4 4 13V19Z"></path></svg>
</span>
</bslib-tooltip><script data-bslib-card-init="">bslib.Card.initializeAllCards();</script></div><div class="card html-fill-item html-fill-container bslib-card" data-title="Flow Rate" data-bslib-card-init="" data-require-bs-caller="card()" data-full-screen="false">
<div class="card-header"><div class="card-title html-fill-item html-fill-container"><span style="display: inline">
Flow Rate
</span></div></div>
<div class="cell card-body html-fill-item html-fill-container">
<div class="cell-output-display html-fill-item html-fill-container">
<div class="plotly html-widget html-widget-output shiny-report-size shiny-report-theme html-fill-item html-fill-container" id="Fig2" style="width:100%;height:300px;"></div>
</div>
<div class="cell-output-display html-fill-item html-fill-container no-overflow-x">
<div id="Tab2" class="shiny-html-output shiny-table-output html-fill-item html-fill-container"></div>
</div>
</div>
<bslib-tooltip placement="auto" bsoptions="[]" data-require-bs-version="5" data-require-bs-caller="tooltip()">
<template>Expand</template>
<span class="bslib-full-screen-enter badge rounded-pill">
<svg xmlns="http://www.w3.org/2000/svg" viewbox="0 0 24 24" style="height:1em;width:1em;" aria-hidden="true" role="img"><path d="M20 5C20 4.4 19.6 4 19 4H13C12.4 4 12 3.6 12 3C12 2.4 12.4 2 13 2H21C21.6 2 22 2.4 22 3V11C22 11.6 21.6 12 21 12C20.4 12 20 11.6 20 11V5ZM4 19C4 19.6 4.4 20 5 20H11C11.6 20 12 20.4 12 21C12 21.6 11.6 22 11 22H3C2.4 22 2 21.6 2 21V13C2 12.4 2.4 12 3 12C3.6 12 4 12.4 4 13V19Z"></path></svg>
</span>
</bslib-tooltip><script data-bslib-card-init="">bslib.Card.initializeAllCards();</script></div>
</div>
<div class="html-fill-item html-fill-container bslib-grid" style="display: grid; grid-template-columns: minmax(3em, 1fr) minmax(3em, 1fr);
grid-auto-rows: minmax(0, 1fr);">
<div class="card html-fill-item html-fill-container bslib-card" data-title="Vascular Resistance" data-bslib-card-init="" data-require-bs-caller="card()" data-full-screen="false">
<div class="card-header"><div class="card-title html-fill-item html-fill-container"><span style="display: inline">
Vascular Resistance
</span></div></div>
<div class="cell card-body html-fill-item html-fill-container">
<div class="cell-output-display html-fill-item html-fill-container">
<div class="plotly html-widget html-widget-output shiny-report-size shiny-report-theme html-fill-item html-fill-container" id="Fig3" style="width:100%;height:300px;"></div>
</div>
<div class="cell-output-display html-fill-item html-fill-container no-overflow-x">
<div id="Tab3" class="shiny-html-output shiny-table-output html-fill-item html-fill-container"></div>
</div>
</div>
<bslib-tooltip placement="auto" bsoptions="[]" data-require-bs-version="5" data-require-bs-caller="tooltip()">
<template>Expand</template>
<span class="bslib-full-screen-enter badge rounded-pill">
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<div class="card-body html-fill-item html-fill-container">
<table class="caption-top table">
<colgroup>
<col style="width: 30%">
<col style="width: 16%">
<col style="width: 32%">
<col style="width: 21%">
</colgroup>
<thead>
<tr class="header">
<th>Class</th>
<th style="text-align: left;">Indicator</th>
<th style="text-align: left;">Meaning</th>
<th style="text-align: left;">Unit</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>Perfusion indicators</td>
<td style="text-align: left;"><span class="math inline">\(md_{sys}\)</span></td>
<td style="text-align: left;">median systolic pressure</td>
<td style="text-align: left;">mmHg</td>
</tr>
<tr class="even">
<td></td>
<td style="text-align: left;"><span class="math inline">\(m_{dia}\)</span></td>
<td style="text-align: left;">mean diastolic pressure</td>
<td style="text-align: left;">mmHg</td>
</tr>
<tr class="odd">
<td></td>
<td style="text-align: left;"><span class="math inline">\(m_{flow}\)</span></td>
<td style="text-align: left;">mean flow rate</td>
<td style="text-align: left;">ml/min</td>
</tr>
<tr class="even">
<td></td>
<td style="text-align: left;"><span class="math inline">\(m_{res}\)</span></td>
<td style="text-align: left;">mean vascular resistance</td>
<td style="text-align: left;">mmHg/ml/min</td>
</tr>
<tr class="odd">
<td></td>
<td style="text-align: left;"><span class="math inline">\(SD_{res}\)</span></td>
<td style="text-align: left;">std. dev. of resistance</td>
<td style="text-align: left;">mmHg/ml/min</td>
</tr>
<tr class="even">
<td></td>
<td style="text-align: left;"><span class="math inline">\(\Delta_{res}\)</span></td>
<td style="text-align: left;">drop in resistance within first 60 min</td>
<td style="text-align: left;">mmHg/ml/min</td>
</tr>
<tr class="odd">
<td></td>
<td style="text-align: left;"><span class="math inline">\(\beta_{res}\)</span></td>
<td style="text-align: left;">drop in resistance per Minute</td>
<td style="text-align: left;">mmHg/ml/min<span class="math inline">\(^2\)</span></td>
</tr>
<tr class="even">
<td>Temperature indicators</td>
<td style="text-align: left;"><span class="math inline">\(m_{ice}\)</span></td>
<td style="text-align: left;">mean ice temperature</td>
<td style="text-align: left;"><span class="math inline">\(\textdegree\)</span>C</td>
</tr>
<tr class="odd">
<td></td>
<td style="text-align: left;"><span class="math inline">\(SD_{ice}\)</span></td>
<td style="text-align: left;">std. dev. of ice temperature</td>
<td style="text-align: left;"><span class="math inline">\(\textdegree\)</span>C</td>
</tr>
<tr class="even">
<td></td>
<td style="text-align: left;"><span class="math inline">\(y_{\text{start}}\)</span></td>
<td style="text-align: left;">perfusate temperature at start</td>
<td style="text-align: left;"><span class="math inline">\(\textdegree\)</span>C</td>
</tr>
<tr class="odd">
<td></td>
<td style="text-align: left;"><span class="math inline">\(m_{perf}\)</span></td>
<td style="text-align: left;">mean perfusate temperature</td>
<td style="text-align: left;"><span class="math inline">\(\textdegree\)</span>C</td>
</tr>
<tr class="even">
<td></td>
<td style="text-align: left;"><span class="math inline">\(SD_{perf}\)</span></td>
<td style="text-align: left;">std. dev. of perfusate temperature</td>
<td style="text-align: left;"><span class="math inline">\(\textdegree\)</span>C</td>
</tr>
<tr class="odd">
<td></td>
<td style="text-align: left;"><span class="math inline">\(\Delta t_{ice>3}\)</span></td>
<td style="text-align: left;">duration ice temp. above 3<span class="math inline">\(\textdegree\)</span>C</td>
<td style="text-align: left;">MM:HH:SS</td>
</tr>
<tr class="even">
<td></td>
<td style="text-align: left;"><span class="math inline">\(\Delta t_{perf>10}\)</span></td>
<td style="text-align: left;">duration perf. temp. above 10<span class="math inline">\(\textdegree\)</span>C</td>
<td style="text-align: left;">MM:HH:SS</td>
</tr>
<tr class="odd">
<td>Quality control</td>
<td style="text-align: left;"><span class="math inline">\(D^2_{perf}\)</span></td>
<td style="text-align: left;">Distance of the case from other cases with respect to perfusion indicators (a lower score is better). It can be seen as the deviation from the norm.</td>
<td style="text-align: left;"><em>unitless</em></td>
</tr>
<tr class="even">
<td></td>
<td style="text-align: left;"><span class="math inline">\(P_{perf}\)</span></td>
<td style="text-align: left;">Percentile rank of <span class="math inline">\(D^2_{perf}\)</span>. For example, a score of 0.90 means that 90% of the cases had a better result (thus, a lower score is better).</td>
<td style="text-align: left;">%</td>
</tr>
<tr class="odd">
<td></td>
<td style="text-align: left;"><span class="math inline">\(D^2_{temp}\)</span></td>
<td style="text-align: left;">Distance of the case from other cases with respect to temperature indicators (a lower score is better). It can be seen as the deviation from the norm.</td>
<td style="text-align: left;"><em>unitless</em></td>
</tr>
<tr class="even">
<td></td>
<td style="text-align: left;"><span class="math inline">\(P_{temp}\)</span></td>
<td style="text-align: left;">Percentile rank of <span class="math inline">\(D^2_{temp}\)</span>. For example, a score of 0.90 means that 90% of the cases had a better result (thus, a lower score is better).</td>
<td style="text-align: left;">%</td>
</tr>
</tbody>
</table>
</div>
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</div><div id="about" class="dashboard-page tab-pane grid-skip html-fill-item html-fill-container" data-orientation="rows" aria-labelledby="tab-about">
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<div class="h4">
About
</div>
<p>EXAM (ex-vivo allograft monitoring) is a dashboard for analyzing hypothermic machine perfusion data from the <a href="https://www.organ-recovery.com/lifeport-kidney-transporter/">ORS LifePort Kidney Transporter</a>. EXAM is free software written in the R programming language.</p>
<div class="h4">
Contact
</div>
<p>For inquiries about EXAM, please get in touch with Simon Schwab <a href="mailto:simon.schwab@swisstransplant.org" class="email">simon.schwab@swisstransplant.org</a>.</p>
<div class="h4">
References
</div>
<p>Schwab S, Steck H, Binet I, et al. EXAM: Ex-vivo allograft monitoring dashboard for the analysis of hypothermic machine perfusion data in deceased-donor kidney transplantation. <em>PLOS Digit Health</em>. 2024;3(12):e0000691. <a href="https://doi.org/10.1371/journal.pdig.0000691">doi:10.1371/journal.pdig.0000691</a></p>
<p>Schwab S. EXAM: Ex-vivo allograft monitoring dashboard. Github; 2025. Accessed February 13, 2025. <a href="https://github.com/Swisstransplant/EXAM" class="uri">https://github.com/Swisstransplant/EXAM</a></p>
<p>Schwab S. swt: Swisstransplant R Package. Github; 2024. Accessed February 13, 2025. <a href="https://github.com/Swisstransplant/swt" class="uri">https://github.com/Swisstransplant/swt</a></p>
<div class="h4">
Acknowledgments
</div>
<p>EXAM was developed by Swisstransplant in collaboration with three Swiss transplant centers.</p>
<div class="{{layout-ncol=4}} html-fill-item html-fill-container">
<p><img src="images/SWT_2955_2021.png" style="float:left; padding:16px" height="80" alt="Surus"> <img src="images/HUG.png" style="float:left; padding:16px" height="80" alt="Surus"> <img src="images/Insel.png" style="float:left; padding:16px" height="80" alt="Surus"> <img src="images/KSSG.png" style="padding:16px" height="80" alt="Surus"></p>
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</div>
</div>
</div></div><aside id="bslib-sidebar-1" class="sidebar html-fill-container html-fill-item"><div class="html-fill-container html-fill-item">
<div class="cell-output-display no-overflow-x">
<div class="form-group shiny-input-container">
<label class="control-label" id="ID-label" for="ID">Select example dataset:</label>
<div>
<select id="ID" class="shiny-input-select"><option value="ST-0003-IceTemp" selected="">ST-0003-IceTemp</option>
<option value="ST-0002-PerfusionTemp">ST-0002-PerfusionTemp</option>
<option value="ST-0001-Perfect">ST-0001-Perfect</option></select>
<script type="application/json" data-for="ID" data-nonempty="">{"plugins":["selectize-plugin-a11y"]}</script>
</div>
</div>
</div>
<div class="cell-output-display">
<div class="form-group shiny-input-container">
<label class="control-label" id="file1-label" for="file1">Upload LifePort data file:</label>
<div class="input-group">
<label class="input-group-btn input-group-prepend">
<span class="btn btn-default btn-file">
Browse...
<input id="file1" class="shiny-input-file" name="file1" type="file" style="position: absolute !important; top: -99999px !important; left: -99999px !important;" accept="text/csv,text/comma-separated-values,text/plain,.csv">
</span>
</label>
<input type="text" class="form-control" placeholder="No file selected" readonly="readonly">
</div>
<div id="file1_progress" class="progress active shiny-file-input-progress">
<div class="progress-bar"></div>
</div>
</div>
</div>
<div class="callout callout-style-simple callout-note callout-titled">
<div class="callout-header d-flex align-content-center collapsed" data-bs-toggle="collapse" data-bs-target=".callout-1-contents" aria-controls="callout-1" aria-expanded="false" aria-label="Toggle callout">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
<span class="screen-reader-only">Note</span>Terms of use
</div>
<div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
</div>
<div id="callout-1" class="callout-1-contents callout-collapse collapse">
<div class="callout-body-container callout-body">
<p>By accessing or using this program, you agree to the terms of the <a href="https://www.gnu.org/licenses/agpl-3.0.html">GNU Affero General Public License</a> and the following supplements to its sections 15 and 16:</p>
<ul>
<li>The program is provided “as is” without warranty or any obligation from Swisstransplant;</li>
<li>Swisstransplant excludes liability for damages, losses, or claims arising from program use, to the extent permitted by law; and</li>
<li>You are solely responsible for evaluating the program’s functionality, suitability, and safety before use.</li>
</ul>
<p>Copyright (C) 2023–2026 Swisstransplant</p>
</div>
</div>
</div>
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<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-2-contents" aria-controls="callout-2" aria-expanded="true" aria-label="Toggle callout">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
<span class="screen-reader-only">Important</span>Important
</div>
<div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
</div>
<div id="callout-2" class="callout-2-contents callout-collapse collapse show">
<div class="callout-body-container callout-body">
<p>Hypothermic machine perfusion data should not be used as a basis for discarding a kidney allograft.</p>
<p>Please refrain from uploading personal, sensitive, or patient-identifiable data. All uploaded data is temporary and will be automatically deleted at the end of the session. The developers assume no liability for any misuse of the application or the data provided by users.</p>
</div>
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<p>
<script type="application/shiny-prerendered" data-context="server-start">
library(fs) # MIT
library(shiny) # GPL-3
suppressPackageStartupMessages(library(plotly)) # MIT
library(swt) # GPL-3
# Quarto MIT
# SWT colors
col = swt_colors()
# load internal example data from package swt
data("exam-examples")
# load swt data instead and overwrite example variables
# PATH_DATA = file.path(path_home(), "OneDrive - Swisstransplant", "Projects", "EXAM", "data")
# load(file.path(PATH_DATA, "exam.RData"))
#
# exam.device = data.device
# exam.organ = data.organ
# exam.sumstats = data.sumstats
# exam.timeseries = data.timeseries
# helper functions for plotly
hline <- function(y = 0, color = "grey", type="dash") {
list(
type = "line",
x0 = 0,
x1 = 1,
xref = "paper",
y0 = y,
y1 = y,
line = list(color = color, dash=type)
)
}
vline <- function(x = 0, color = "grey", type="dash") {
list(
type = "line",
y0 = 0,
y1 = 1,
yref = "paper",
x0 = x,
x1 = x,
line = list(color = color, dash=type)
)
}
</script>
<script type="application/shiny-prerendered" data-context="server">
# I need reactive value because the dataset can either be from
# 1) the internal data or
# 2) the file upload
dataset = reactiveVal()
# 1) select dataset from internal example data from package swt
observeEvent(input$ID, {
i = which(exam.organ$ID == input$ID)
# I create a data list from the internal data
dataset(list(data.device = exam.device[i,],
data.organ = exam.organ[i,],
data = exam.timeseries[[i]],
data.sumstats = exam.sumstats[i,]))
})
# 2) read data from file upload
observeEvent(input$file1, {
# read data, processing and sumstats
# error handling when damaged lifeport data file is uploaded
lp_data = tryCatch({
lp_data = lifeport_read(file = input$file1$datapath, format = "guess")
lp_data = lifeport_process(lp_data)
lp_data = lifeport_sumstats(lp_data)
lp_data$data.organ$ID = gsub("\\.txt$|\\.TXT$", "", basename(input$file1$name))
# Calculate quality indicator
# subset variables: 7 dimensions
tmp.perf = subset(lp_data$data.sumstats, select = c("systolicPressure.md",
"diastolicPressure.mean",
"flowRate.mean",
"organResistance.mean",
"organResistance.sd"))
tmp.temp = subset(lp_data$data.sumstats, select = c("iceContainerTemperature.mean",
"iceContainerTemperature.sd",
"infuseTemperature.start",
"infuseTemperature.mean",
"infuseTemperature.sd"))
# calculate D^2
stats = lifeport_d2(data = tmp.perf, type = "perf")
lp_data$data.sumstats$D2perf = stats$d2
lp_data$data.sumstats$Pperf = stats$rank
stats = lifeport_d2(data = tmp.temp, type = "temp")
lp_data$data.sumstats$D2temp = stats$d2
lp_data$data.sumstats$Ptemp = stats$rank
dataset(lp_data)
}, error = function(e) {
showModal(modalDialog(
title = "Error reading file",
"The file does not contain valid LifePort data. Maybe you selected the wrong file or the file has been damaged.",
easyClose = FALSE
))
})
})
# Figure 1: Pressure Chart
output$Fig1 <- renderPlotly({
# lst = lp_data # for debugging
lst = dataset() # data is a list
# converting from wide to long
d = data.frame(pressure = c(lst$data$SystolicPressure.flt,
lst$data$DiastolicPressure.flt),
time.clock = c(lst$data$time.clock,
lst$data$time.clock),
group = c(rep("Systolic pressure", nrow(lst$data)),
rep("Diastolic pressure", nrow(lst$data))))
d$group = factor(d$group, levels = c("Systolic pressure", "Diastolic pressure"))
# figure
fig = plot_ly(d, x=~time.clock, y=~pressure, type="scatter", mode="lines",
color=~group, colors = c(col$blue.swt, col$darkyellow.kidney))
fig = fig %>% layout(yaxis = list(title = "mmHg", range = c(0, 45)),
xaxis = list(title = "Time"),
legend = list(orientation = 'h', yanchor = "bottom",
y = 1.02, x = 1, xanchor = "right"),
shapes = list(hline(20), hline(30))
)
})
# Figure 2: Flow Rate Chart
output$Fig2 <- renderPlotly({
# lst = lp_data # for debugging
lst = dataset() # data is a list
d = lst$data
# handle timeseries shorter than 30 min.
if(length(d$time.clock) >= 181) {
t_30 = d$time.clock[181]
} else {
t_30 = d$time.clock[length(d$time.clock)]
}
# figure
fig = plot_ly(d, x=~time.clock, y=~FlowRate.flt, type="scatter", mode="lines",
color="all", colors = col$blue.swt)
fig = fig %>% layout(yaxis = list(title = "ml/min", range = c(0, 200)),
xaxis = list(title = "Time"),
shapes = list(hline(100),
vline(t_30, type="dot"))
)
})
# Figure 3: Flow Rate Chart
output$Fig3 <- renderPlotly({
# lst = lp_data # for debugging
lst = dataset() # data is a list
d = lst$data
s = lst$data.sumstats
# handle timeseries shorter than 30 min.
if(length(d$time.clock) >= 181) {
t_30 = d$time.clock[181]
} else {
t_30 = d$time.clock[length(d$time.clock)]
}
# figure
fig = plot_ly(d, x=~time.clock, y=~OrganResistance.flt, type="scatter", mode="lines",
color="all", colors = col$blue.swt, name = "Vascular resistance")
# don't show slope when there are no x1, y1 and x2, y2 values
if (!is.na(s$organResistance.x1) & !is.na(s$organResistance.y1) &
!is.na(s$organResistance.x1) & !is.na(s$organResistance.y1) ) {
fig = fig %>% add_trace(x = c(d$time.clock[s$organResistance.x1],
d$time.clock[s$organResistance.x2]),
y = c(s$organResistance.y1, s$organResistance.y2),
mode = "markers+lines", color = I(col$strongred.akzent), name = "Slope")
}
fig = fig %>% layout(yaxis = list(title = "mmHg/ml/min", range = c(0, 0.5)),
xaxis = list(title = "Time"),
legend = list(orientation = 'h', yanchor = "bottom",
y = 1.02, x = 1, xanchor = "right"),
shapes = list(hline(0.10),
hline(0.30),
vline(t_30, type="dot")
)
)
})
# Figure 4: Temperature Chart
output$Fig4 <- renderPlotly({
HIGH_INF_TEMP = 10
HIGH_ICE_TEMP = 3.0
CODE_HIGHTEMP = 4096
CODE_TEMPSHUTDOWN = 8192
lst = dataset() # data is a list
# prepare time series of ice and perf temp too high
is_high_perf = lst$data$InfuseTemperature > HIGH_INF_TEMP &
lst$data$FlowRate.flt > 5 & !is.na(lst$data$FlowRate.flt)
high_perf = lst$data$InfuseTemperature
high_perf[!is_high_perf] = NA
is_high_ice = lst$data$IceContainerTemperature > HIGH_ICE_TEMP
high_ice = lst$data$IceContainerTemperature
high_ice[!is_high_ice] = NA
# converting from wide to long
d = data.frame(temperature = c(lst$data$IceContainerTemperature,
lst$data$InfuseTemperature,
high_perf,
high_ice),
time.clock = rep(lst$data$time.clock, 4),
group = c(rep("Ice temperature", nrow(lst$data)),
rep("Perfusate temperature", nrow(lst$data)),
rep("High temperature", nrow(lst$data)),
rep("High temperature", nrow(lst$data))
))
d$group = factor(d$group, levels = c("Ice temperature",
"Perfusate temperature",
"High temperature"))
# figure
fig = plot_ly(d, x=~time.clock, y=~temperature, type="scatter", mode="lines",
color=~group, colors = c(col$blue.swt,
col$darkyellow.kidney,
col$strongred.akzent))
fig = fig %>% layout(yaxis = list(title = "Degrees Celsius", range = c(0, 20)),
xaxis = list(title = "Time"),
legend = list(orientation = 'h', yanchor = "bottom",
y = 1.02, x = 1, xanchor = "right"),
shapes = list(hline(5), hline(10))
)
# Add high temperature events
if (CODE_HIGHTEMP %in% lst$data$Error2) {
i = which(lst$data$Error2 == CODE_HIGHTEMP)[1]
fig = fig %>% add_markers(x = lst$data$time.clock[i], y = lst$data$IceContainerTemperature[i]-2,
marker = list(symbol = "triangle-up", size = 14, color = "orange"),
name = "Ice alert", inherit = FALSE)
}
# also sometimes contained in Error1, but not often
if (CODE_HIGHTEMP %in% lst$data$Error1) {
i = which(lst$data$Error1 == CODE_HIGHTEMP)[1]
fig = fig %>% add_markers(x = lst$data$time.clock[i], y = lst$data$IceContainerTemperature[i]-2,
marker = list(symbol = "triangle-up", size = 14, color = "orange"),
name = "Ice alert", inherit = FALSE)
}
# Add temperature shutdown
if (CODE_TEMPSHUTDOWN %in% lst$data$Error1) {
i = which(lst$data$Error1 == CODE_TEMPSHUTDOWN)[1]
fig = fig %>% add_markers(x = lst$data$time.clock[i], y = lst$data$IceContainerTemperature[i]-2,
marker = list(symbol = "triangle-up", size = 14, color = "red"),
name = "High temp. shutdown", inherit = FALSE)
}
fig
})
# Info table
output$Tab_info <- renderTable({
lst = dataset()
tab = cbind(lst$data.organ[, "ID"],
lst$data.device[, c("SerialNumber", "UnitID", "StartTime",
"StopTime", "Runtime")],
lst$data.sumstats[, "perfusion.dur.str"]
)
colnames(tab) = c("File ID", "Serial no.", "Unit ID",
"Start time", "Stop time", "Run time", "Perfusion time")
tab
})
# Tables with Summary statistics
output$Tab1 <- renderTable({
lst = dataset()
tab = lst$data.sumstats[, c("systolicPressure.md", "diastolicPressure.mean")]
colnames(tab) = c("<i>md<\u002fi><sub>sys<\u002fsub>", "<i>m<\u002fi><sub>dia<\u002fsub>")
tab
}, sanitize.text.function = function(x) x) # needed for formatting special characters
output$Tab2 <- renderTable({
lst = dataset()
tab = lst$data.sumstats[, "flowRate.mean", drop = FALSE]
colnames(tab) = c("<i>m<\u002fi><sub>flow<\u002fsub>")
tab
}, sanitize.text.function = function(x) x) # needed for formatting special characters
output$Tab3 <- renderTable({
lst = dataset()
tab = lst$data.sumstats[, c("organResistance.mean", "organResistance.sd",
"organResistance.delta","organResistance.slope"), drop = FALSE]
colnames(tab) = c("<i>m<\u002fi><sub>res<\u002fsub>", "<i>SD<\u002fi><sub>res<\u002fsub>",
"<i>Δ<\u002fi><sub>res<\u002fsub>", "<i>β<\u002fi><sub>res<\u002fsub>")
tab
}, sanitize.text.function = function(x) x) # needed for formatting special characters
output$Tab4 <- renderTable({
lst = dataset()
tab = lst$data.sumstats[, c("iceContainerTemperature.mean","iceContainerTemperature.sd",
"iceContainerTemperature.minAbove.str", "infuseTemperature.start",
"infuseTemperature.mean", "infuseTemperature.sd",
"infuseTemperature.minAbove.str")]
colnames(tab) = c("<i>m<\u002fi><sub>ice<\u002fsub>", "<i>SD<\u002fi><sub>ice<\u002fsub>",
"<i>Δt<\u002fi><sub>y>3<\u002fsub>", "<i>y<\u002fi><sub>start<\u002fsub>",
"<i>m<\u002fi><sub>perf<\u002fsub>", "<i>SD<\u002fi><sub>perf<\u002fsub>",
"<i>Δt<\u002fi><sub>y>10<\u002fsub>")
tab
}, sanitize.text.function = function(x) x) # needed for formatting special characters
# Table Quality Control
output$Tab_qual <- renderTable({
lst = dataset()
tab = cbind(
lst$data.organ[, c("OrganID", "KidneySide")],
lst$data.sumstats[, c("D2perf", "Pperf", "D2temp", "Ptemp")]
)
tab$Pperf = sprintf("%.0f%%", tab$Pperf*100)
tab$Ptemp = sprintf("%.0f%%", tab$Ptemp*100)
colnames(tab) = c("Organ ID entry", "Kidney side entry",
"<i>D<\u002fi><sup>2<\u002fsup><sub>perf<\u002fsub>",
"<i>P<\u002fi><sub>perf<\u002fsub>",
"<i>D<\u002fi><sup>2<\u002fsup><sub>temp<\u002fsub>",
"<i>P<\u002fi><sub>temp<\u002fsub>")
tab
}, sanitize.text.function = function(x) x) # needed for formatting special characters
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ojs_define <- function(..., .session = shiny::getDefaultReactiveDomain()) {
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}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
// target, if specified
link.setAttribute("target", "_blank");
if (link.getAttribute("rel") === null) {
link.setAttribute("rel", "noopener");
}
// default icon
link.classList.add("external");
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start',
};
if (contentFn) {
config.content = contentFn;
}
if (onTriggerFn) {
config.onTrigger = onTriggerFn;
}
if (onUntriggerFn) {
config.onUntrigger = onUntriggerFn;
}
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i<noterefs.length; i++) {