Navigate the analysis results

In this documentation, all panels would be marked with Bold Italic, any components (buttons, sliders, menus) in the tool would be marked with code format. Similar to before, the file names are also marked with code format.

There are five components of the Higashi-vis tool:

1. Contact maps visualization panel, which visualizes contact maps of the selected single cell(s)
2. Embedding visualization panel, which visualizes the embedding vectors with various visualization methods (e.g. PCA, UMAP, TSNE, etc.) and provided color schemes (e.g. cell types, batch id, etc.)
3. Control panel, which controls data selection, visualization method, visualization style, etc.
4. Information display panel, which provides feedbacks from the Higashi-vis server. Usually, a message would be displayed before and after a time-consuming step (e.g. UMAP) to ensure the user that the visualization session is not frozen but rather waiting for the computation to finish.
5. Statistics visualization panel, which visualizes statistics of the total cell population and selected cell population. The variable it visualizes is synchronized with the color of the scatter plot.

Now, let's start to use Higashi-vis! The tutorial would include the following contents:

• Dataset selection
• Embeddings visualization
• Synchronized navigation of contact maps
• Contact map style configuration
• Other components

If you feel any part of the Higashi-vis is not clearly explained or any suggestions in general, feel free to raise an issue in the Github repo.