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CHANGELOG.html
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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Changelog • cellengine</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<a class="navbar-link" href="index.html">cellengine</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.0</span>
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<h1>Changelog</h1>
</div>
<div id="changelog" class="section level1">
<p>All notable changes to this project will be documented in this file.</p>
<p>The format is based on <a href="https://keepachangelog.com/en/1.0.0/" class="external-link">Keep a Changelog</a>, and this project adheres to <a href="https://semver.org/spec/v2.0.0.html" class="external-link">Semantic Versioning</a>.</p>
<div class="section level2">
<h2 id="v1-release-candidate">[v1 Release Candidate]<a class="anchor" aria-label="anchor" href="#v1-release-candidate"></a></h2>
<p>v1 will be the first stable release of the CellEngine R toolkit and has several breaking changes compared to the pre-release version.</p>
<div class="section level3">
<h3 id="added">Added<a class="anchor" aria-label="anchor" href="#added"></a></h3>
<ul><li>
<code><a href="reference/createCompensation.html">createCompensation()</a></code> function</li>
<li>
<code><a href="reference/getCompensation.html">getCompensation()</a></code> function</li>
<li>
<code><a href="reference/updateCompensation.html">updateCompensation()</a></code> function</li>
<li>
<code><a href="reference/deleteCompensation.html">deleteCompensation()</a></code> function</li>
<li>All functions now consistently accept <code><a href="reference/byName.html">byName()</a></code> expressions for any ID parameter.</li>
<li>Support for transfers to S3 to <code><a href="reference/getEvents.html">getEvents()</a></code>
</li>
<li>
<code>PER_FILE</code> compensation constant</li>
<li>Support for <code>geometricMean</code> as a statistics value in <code><a href="reference/getStatistics.html">getStatistics()</a></code>.</li>
<li>Support for <code>layout</code> argument in <code><a href="reference/getStatistics.html">getStatistics()</a></code>.</li>
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<h3 id="changed">Changed<a class="anchor" aria-label="anchor" href="#changed"></a></h3>
<ul><li>
<strong>Breaking</strong> Failed API requests will now stop instead of warn.</li>
<li>
<strong>Breaking</strong> <code><a href="reference/getEvents.html">getEvents()</a></code> now uses <code>check.names=FALSE</code>, so data.frame column names will be identical to the parameter names found in the FCS file. For example, “CD4 (Ax647-A)” will no longer be converted to “CD4..Ax647.A.”.</li>
<li>
<strong>Breaking</strong> <code><a href="reference/getEvents.html">getEvents()</a></code> now defaults to <code>headerQ=TRUE</code>, so data.frames will have column names by default now.</li>
<li>
<strong>Breaking</strong> In <code><a href="reference/getEvents.html">getEvents()</a></code>, the argument <code>clamp_q</code> was renamed to <code>clampQ</code>.</li>
<li>
<strong>Breaking</strong> The default for the <code>createPopulation</code> parameter of gate creation functions was changed to <code>is.null(fcsFileId)</code>.</li>
<li>
<strong>Breaking</strong> <code><a href="reference/getCompensations.html">getCompensations()</a></code> now returns a list of lists, with the <code>spillMatrix</code> formatted as a matrix.</li>
<li>
<strong>Breaking</strong> All functions now return lists instead of data.frames. (In the future, the lists may be changed to S3 classes.)</li>
<li>
<strong>Breaking</strong> The <code>xVertices</code> and <code>yVertices</code> parameters of <code>createPolygonGate</code> are replaced <code>vertices=list(c(x1, y1), c(x2, y2), c(x3, y3))</code>.</li>
<li>
<strong>Breaking</strong> The <code>create__Gate()</code> functions previously had two parameters for specifying the FCS file for tailoring (<code>fcsFileId</code> and <code>fcsFile</code>) and two parameters for specifying the parent population (<code>parentPopulationId</code> and <code>parentPopulation</code>), with the latter parameters performing a lookup by name. To be consistent with the rest of the toolkit, <code>fcsFile</code> and <code>parentPopulation</code> have been removed. Instead, use <code><a href="reference/byName.html">byName()</a></code> expressions, e.g. <code>createRectangleGate(..., fcsFileId=byName("Sample1.fcs"), parentPopulationId=byName("CD3+"), ...)</code>.</li>
<li>
<code><a href="reference/createQuadrantGate.html">createQuadrantGate()</a></code> and <code><a href="reference/createSplitGate.html">createSplitGate()</a></code> accept either <code>createPopulation</code>, singular, for consistency with other <code>create__Gate</code> functions; or <code>createPopulations</code>, plural, to accurately reflect the behavior.</li>
<li>
<code>getStatistics(fcsFileIds=NULL, ...)</code> should return statistics for all non-control FCS files.</li>
<li>
<code><a href="reference/getStatistics.html">getStatistics()</a></code> should support <code>percentOf=c("PARENT")</code>.</li>
<li>
<code>getSTatistics(populations=c("pop1", "pop2", ...))</code> should return statistics for all specified populations.</li>
</ul></div>
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<h3 id="removed">Removed<a class="anchor" aria-label="anchor" href="#removed"></a></h3>
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<p></p><p>Developed by Zach Bjornson, Gerrit Egnew.</p>
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