Several updates and adjustments

docs/index.html

@@ -92,11 +92,12 @@ <h2 id="introduction">Introduction</h2>
 <p><strong>Cell Journey</strong> is an open-source tool for interactive exploration and analysis of single-cell trajectories. It allows operating in three-dimensional space at the level of the entire dataset and individual cells. Each implemented visualization comes with several parameters, allowing versatile and quick customization. The resulting graphs can be saved as raster graphics, vector graphics, or interactive visualization in a standalone html file format.</p>
 <h3 id="features">Features</h3>
 <ul>
-<li>Analyze datasets in csv, h5ad, and h5mu formats.</li>
-<li>Visualize 3D scatter plots, cone plots, streamlines, and streamlets.</li>
 <li>Quick and straightforward configuration.</li>
-<li>Data filtering along with various plot customizations.</li>
 <li>Explore multiple features simultaneously.</li>
+<li>Analyze datasets in csv, h5ad, and h5mu formats.</li>
+<li>Data filtering along with various plot customizations.</li>
+<li>Visualize 3D scatter plots, cone plots, streamlines, and streamlets.</li>
+<li>Represent feature activity values in a 3D embedding by volume plots.</li>
 <li>Automated differential gene expression analysis for calculated trajectories.</li>
 <li>Save publication-ready figures as well as interactive visualizations.</li>
 </ul>
@@ -153,5 +154,5 @@ <h3 id="demo">Demo</h3>
 
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+Build Date UTC : 2024-11-05 12:12:16.851229+00:00
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docs/install.html

@@ -119,7 +119,7 @@ <h3 id="3-install-dependencies">3. Install dependencies</h3>
 <p>Cell Journey is based on many libraries that are necessary for the toolkit to run correctly. These dependencies can be installed using the command</p>
 <pre><code class="language-bash">pip install -r /path/to/celljourney/requirements.txt
 </code></pre>
-<p>Please replace the example path <code>/path/to/celljourney/</code> with one corresponding to your system's Cell Journey location. Remember to install the dependencies <strong>after</strong> activating the virtual environment.</p>
+<p>Please replace the example path <code>/path/to/celljourney/</code> with one corresponding to your system's Cell Journey location. Remember to install the dependencies after activating the virtual environment.</p>
 <h3 id="4-run-the-main-script">4. Run the main script</h3>
 <p>To run Cell Journey, you need to run the python script <code>celljourney.py</code></p>
 <pre><code class="language-bash">python /path/to/celljourney/celljourney.py
@@ -129,7 +129,7 @@ <h3 id="4-run-the-main-script">4. Run the main script</h3>
 <pre><code class="language-bash">python celljourney.pl --port 8081
 </code></pre>
 <p>If the default or user-designated port is already occupied, the program will not run. If the user wants to run several Cell Journey sessions simultaneously, a different port should be designated for each session.</p>
-<p>To terminate the program, you must abort the <code>celljourney.py</code> script. This can be done in the shell where the script was run using the <code>ctrl+z</code> key combination.</p>
+<p>To terminate the program, you must abort the <code>celljourney.py</code> script. This can be done in the shell where the script was run using the <code>ctrl+c</code> key combination.</p>
 
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docs/usage.html

@@ -111,7 +111,7 @@
                 <h2 id="usage">Usage</h2>
 <h3 id="upload-data-and-select-coordinates">Upload data and select coordinates</h3>
 <p>To upload a dataset, use the <code>Drag and drop or select a file to upload</code> button and then click on <code>Upload data</code>. After the data is uploaded correctly, a confirmation message will appear. If the uploaded data is not normalized, an additional window will appear that will allow you to do so. Next, select the appropriate features with cell coordinates and the corresponding velocity vector components. Click on the <code>Submit selected coordinates</code> button to confirm your selection. The Scatter Plot and Cone Plot sections will update automatically.</p>
-<p><strong>Very important!</strong> When uploading your data, ensure it is located in the same directory as the celljourney.py file (the framework Cell Journey is based on cannot get the uploaded data's full path). To overcome this limitation, you can use the <code>--file</code> flag when running the software, e.g.</p>
+<p>There is also an alternative way to upload the file by specifying the path directly on the command line with the <code>--file</code> flag, e.g.</p>
 <pre><code>python celljourney.py --file=/data/projects/sequencing/file.h5ad
 </code></pre>
 <h3 id="global-plot-configuration">Global plot configuration</h3>