Documenting the explore ui

doc/explore.rst

+Explore the data
+================
+
+.. contents:: Table of Contents
+   :depth: 3
+
+
+
+Here is the exploration page, on this page we will be able to narrow your exploration to hosts/viruses/data sources. A key notion is to understand is `What is a relevant hosts/viruses/data sources`_ . Once understood you are good to go for exploring the database. With `Advanced options`_, you can adjust the filtering criteria and rendering options, and also apply analytics tool.
+
+
+.. image:: _static/explore-ui.png
+  :width: 100%
+  :alt: Main interface to explore the responses
+
+
+What is a relevant hosts/viruses/data sources
+---------------------------------
+
+A host/virus/data source is relevant if it has at least one response associated with at least one of the selected elements. It means that if you selected  a data source, relevant viruses and hosts are the ones in this data source, while if you select a virus, a relevant host has at least one response with this virus, and the data source where this response can be found is also relevant.
+
+
+Example
+~~~~~~~
+
+Let us consider that:
+
+- data source :math:`d_1` document the response of host :math:`h` to virus :math:`v_1` and virus :math:`w`
+- data source :math:`d_2` document the response of host :math:`h` to virus :math:`v_2`.
+
++---------------------------+---------------------------------------------------------------+
+| Element(s) selected       | Element(s) relevant                                           |
++---------------------------+---------------------------------------------------------------+
+| :math:`d_1`               | :math:`v_1`, :math:`w`, :math:`h`                             |
++---------------------------+---------------------------------------------------------------+
+| :math:`h`                 | :math:`d_1`, :math:`d_2`, :math:`v_1`, :math:`v_2`, :math:`w` |
++---------------------------+---------------------------------------------------------------+
+| :math:`h` and :math:`v_1` | :math:`d_1`                                                   |
++---------------------------+---------------------------------------------------------------+
+| :math:`w` and :math:`d_2` | none                                                          |
++---------------------------+---------------------------------------------------------------+
+
+
+
+Advanced options
+---------------------------------
+We regrouped as advanced option the `Analysis Tools`_ such as infection ratio, the `Data filtering options`_ allowing you for example to focus on data source associated to a publication, and finally the `Rendering options`_ such as adaptive cell background based on the agreement (or not) of data source on the response in this cell.
+
+
+All selected options are stack-up under the selection area allowing you both to easily remove them, and to quickly know what is rendered when you arrive on this page from link sharing.
+
+.. image:: _static/option-stacked.png
+  :width: 100%
+  :alt: option stacked
+
+
+**Quick tip**
+~~~~~~~~~~~~~~~~~~~~~
+
+
+To keep the `Advanced options`_ pane opened, just click on the lock.
+
+
+
+.. image:: _static/advanced-options-lock.png
+  :alt: advanced-options-lock
+  :align: center
+
+
+Analysis Tools
+~~~~~~~~~~~~~~~~~~~~~
+- | **Consider all positive response as a infection**
+  | The global scheme of responses allows to express an intermediate infection, you can thus consider that an intermediate infection is or is not an infection.
+
+- | **Show the infection ratio for the viruses**
+  | Considering the hosts and data source you have selected, the infection is the percentage of hosts for which an infection is documented.
+
+- | **Show the infection ratio for the hosts**
+  | *same as virus*.
+
+- | **Hide  virus without any infection**
+  | You can can also hide viruses that have no infection associated to the selected data source and host.
+
+- | **Hide  host without any infection**
+  | *same as virus*.
+
+- | **Consider that there is an infection only when all data sources documenting the interaction observed an infection**
+| Different data sources can disagree on whether a given virus has infected or not a given host. You have the possibility to consider that there is an infection only when all data source agree on it.
+
+Data filtering options
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+These options allows you to narrow you exploration to data associated to a publication (**Only published data**), to viruses that have an identifier (**Only identified viruses**), or hosts (**Only identified hosts**), and restrict to only one **life domain**.
+
+Rendering options
+~~~~~~~~~~~~~~~~~~~~~
+
+.. _rendering-option-label:
+
+- | **Display all the table at once, even if it does not fit on screen**
+  | The whole the 2D array of responses does not always fit to the screen, we thus use scroll bar to provide a better user experience. You can render the whole 2D array at once without scroll if you want, it is useful for screenshot purpose.
+
+- | **Render table focusing on disagreements**
+  | When two data sources disagree on the response associated to a pair of host and virus, the cell is bordered in black, you can increase this highlighting by fading other agreeing cells.
+
+.. image:: _static/normal-vs-focus.png
+  :alt: Main interface to explore the responses
+  :align: center
+
+
+
+
+
+
+

doc/index.rst

@@ -12,7 +12,7 @@ If you found a bug, do not hesitate to submit an issue in the `issue tracking sy
    :maxdepth: 2
    :caption: Contents:
 
-   tutorial
+   explore
    data_import
    compatible_file