1. Visualization tool

Comparison of Plotly and ECharts for Visualizing Backend Results

Plotly

Advantages:

1. Simplicity and User-Friendliness:

   • Plotly is renowned for its user-friendly API, making it easy to create interactive charts.
   • Ideal for quickly implementing standard charts without extensive configuration.

2. Interactive Charts:

   • Plotly provides comprehensive interactivity by default, including zooming, panning, and hover effects.
   • These interactive features make Plotly an excellent choice for dashboards that require deep data interactions.

3. Extensive Documentation and Community Support:

   • Plotly boasts extensive documentation and a large user community, facilitating learning and troubleshooting.
   • It supports a wide range of chart types, including complex 3D charts.

4. Seamless Integration with Dash:

   • Plotly integrates seamlessly with Dash, a web application for building dashboards, also developed by Plotly.
   • This integration simplifies creating complex dashboards in Python.

Disadvantages:

1. Performance:
   • Plotly can become slower in rendering and interactivity with very large datasets.
   • This might be a limitation for very large sets of data to visualize.

ECharts

Advantages:

1. Performance and Speed:

   • ECharts is known for its high performance, especially when handling and visualizing large datasets.
   • It uses WebGL for 3D rendering, beneficial for complex visualizations.

2. Flexibility and Customization:

   • ECharts offers extensive flexibility and customization options, ideal for tailored visualizations.
   • It supports a wide array of visual effects and layouts that can be finely tuned.

3. Modern and Attractive Aesthetics:

   • ECharts provides stylish and modern charts that can be more visually appealing.
   • The default styles are generally more refined and require less tweaking.

4. Open Source and Free:

   • ECharts is fully open-source and free to use, even for commercial projects.

Disadvantages:

1. Complexity and Learning Curve:

   • ECharts' API can be more complex, presenting a steeper learning curve, especially for beginners.
   • Its high flexibility often requires more configuration to create simple charts.

2. Documentation and Support:

   • Although ECharts has good documentation, it can be less intuitive compared to Plotly.
   • It can be more challenging to find specific information for certain use cases.

Decision: Plotly

After weighing the pros and cons of both libraries, we have decided to proceed with Plotly. Here are our reasons:

• User-Friendliness: Plotly allows us to quickly create interactive charts without extensive setup. This speeds up development time and makes it easier for new team members to get up to speed.
• Interactive Features: Plotly's high level of built-in interactivity is ideal for our use cases, which require users to deeply engage with the data.
• Integration with Dash: As we plan to build dashboards that integrate seamlessly with Python, Plotly's integration with Dash provides a significant advantage.
• Documentation and Support: Plotly's comprehensive documentation and large community make development and troubleshooting much easier.

2. Ideas for visualization:

Graph with intensity value:

• can be taken directly from the .wig file
• Issue:
  • Might not be helpful visually if the amount of bases is too big

Graph with intensity value (histogram):

• vertical lines indicate TSSs
• bins might visualize TSSs better from a user perspective
• Issues:
  • How to scale the graph? What if the user wants to look at say a 1000 bases at time?
    -> Zooming in and out cant change the number of bins too much because then we would end up with the graph above
    -> instead more values should make up one bin the more zoomed out the graph is

our TSS comparison vs. TSSpredator Graph:

• Graph with complete sequence and TSSs of TSSpredator and our TSSs in different colors for direct comparison

Venn diagram:

• Demonstrating the commonalities and differences between our prediction and TSSpredators in numbers for example
  • total number of TSSs