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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
<html>
<title>About</title>
<h3>About PlotTwist</h3>
<p>The PlotTwist Shiny app plots the data and statistics of continuous data, with a focus on data from timelapse experiments. Several different options for plotting are available; lineplot, small multiples and heatmap. Summary statistics (mean) and inferential statistics (confidence intervals) can be displayed as well. The user has full control over the visibility of the raw data and statistics by adjustment of the transparency (alpha).
More details about the PlotTwist app can be found in our <a href="https://doi.org/10.1101/745612">preprint</a>.</br>
</p>
<p>To facilitate the display of heterogeneous responses (e.g. from measurements on multiple objects) the user can plot the data as 'small multiples' or in a heatmap style. Some background on these dataviz styles can be found in <a href="http://thenode.biologists.com/visualizing-heterogeneity-of-imaging-data/research/">this blog</a></p>
<p>The data can be supplied in spreadsheet/long format (e.g. by copy-pasting from excel). Multiple file upload is supported and can be used to upload data from different conditions that can be individually colored or displayed. The data is converted into tidy format to enable plotting with ggplot2. Direct import of tidy data is also supported. For more information on the conversion of spreadsheet data to tidy data see <a href="http://thenode.biologists.com/converting-excellent-spreadsheets-tidy-data/education/">this blog</a>.</p>
<p>The web tool offers several options for the <i>normalization</i> of data. Normalization is usually performed to facilitate comparison of different measurements. Background on several normalization methods and their application can be found in <a href="http://thenode.biologists.com/data-normalization/research/">this blog</a>.</p>
<p>One of the unique features of this app is that the settings can be stored, enabling reproducible plots. When you are happy with the plot, use the 'clone current setting' button (upper right button in the plot tab). This will provide a URL that can be stored or bookmarked. The URL stores all the user-defined settings and can be used to retrieve the stored layout. As an example, a styled plot can be retrieved by clicking <a href="https://huygens.science.uva.nl/PlotTwist/?data=2;TRUE;;fold;1,5;&vis=dataasline;0;TRUE;TRUE;1;;&layout=%20;;TRUE;;0.95,1.22;TRUE;TRUE;6;X;600;600&color=none&label=;;TRUE;Time%20%5bminutes%5d;Activity%20%5barbitrary%20units%5d;TRUE;24;24;18;8;;;TRUE&stim=TRUE;bar;0,1.7,1.8,10;baseline,Sphingosine%201-Phosphate;black,grey40&">this link</a>, which represents this hyperlink:
</br>
https://huygens.science.uva.nl/PlotTwist/?data=2;TRUE;;fold;1,5;&vis=dataasline;0;TRUE;TRUE;1;;&layout=%20;;TRUE;;0.95,1.22;TRUE;TRUE;6;X;600;600&color=none&label=;;TRUE;Time%20%5bminutes%5d;Activity%20%5barbitrary%20units%5d;TRUE;24;24;18;8;;;TRUE&stim=TRUE;bar;0,1.7,1.8,10;baseline,Sphingosine%201-Phosphate;black,grey40&</p>
<p>The plot can be saved as a PNG file or a PDF file, which can be opened and edited with Adobe Illustrator to allow for fine adjustments of the lay-out.</p>
<h4>Contact</h4>
<p>PlotTwist is created and maintained by Joachim Goedhart and Marten Postma</br>
Bug reports and feature requests can be communicated in several ways:
<ul>
<li>Github: <a href="https://github.com/JoachimGoedhart/PlotTwist/issues">PlotTwist/issues</a></li>
<li>Twitter: <a href="https://twitter.com/joachimgoedhart">@joachimgoedhart</a></li>
<li>Email: <a href="mailto:
j.goedhart@uva.nl">j.goedhart@uva.nl</a></li>
</ul>
<h4>Source</h4>
Source code is available at <a href="https://github.com/JoachimGoedhart/PlotTwist">github/JoachimGoedhart</a>
</br>
Please cite our work if you use the app: "PlotTwist: A web app for plotting and annotating continuous data" - doi: <a href="https://doi.org/10.1371/journal.pbio.3000581">10.1371/journal.pbio.3000581</a>
</br>
</p>
<h4>Credits</h4>
<p>The code for the shiny app is partially derived from <a href="https://github.com/gertstulp/ggplotgui">ggplotGUI</a>
by <a href="https://www.gertstulp.com">Gert Stulp</a></br>
The colorblind safe palettes were developed by <a href="https://personal.sron.nl/~pault/">Paul Tol</a> and <a href="http://jfly.uni-koeln.de/color/">Okabe and Ito</a>.</p>
</br>
</html>