Add connectivity manual

docs/usage/connectivity.md

+# Connectivity matrix
+
+One of the new features from the Interactive Viewer's [version 2.1.0](https://interactive-viewer-user-documentation.apps.hbp.eu/releases/v2.1.0/) is to explore connectivity data, based on the parcellation area (region). Source of connectivity data is specific dataset(s) from HBP Knowledge Graph.
+
+For now, connectivity data is explorable for parcellation: "JuBrain Cytoarchitectonic Atlas" which is available on "MNI Colin 27" and "ICBM 2009c Nonlinear Asymmetric" template spaces.
+
+## Explore area connectivity
+Select parcellation "JuBrain Cytoarchitectonic Atlas" and click on a region to bring up a context-specific menu
+
+[![](images/region_menu_with_connectivity.png)](images/region_menu_with_connectivity.png)
+
+By clicking on the "Connectivity" button, available datasets for connectivity will be displayed
+
+[![](images/connectivity_dataset_menu.png)](images/connectivity_dataset_menu.png)
+
+From the picture above, connectivity is available from the dataset "1000 Brain Study". Click on a dataset name to explore connectivity data and color visualization on the parcellation.
+After selecting the desired dataset you can mention several changes:
+
+1. Color map for parcellation regions will be changed by connectivity data. (The selected area is marked on the image below)
+    
+    - Color map before selecting connectivity
+    
+   [![](images/connectivity_color_before.png)](images/connectivity_color_before.png)
+    
+    - Color map after selecting connectivity
+    
+   [![](images/connectivity_color_after.png)](images/connectivity_color_after.png)
+
+2. A Side panel will be opened (If it is closed) and connectivity data will be displayed
+
+   [![](images/connectivity_data_main.png)](images/connectivity_data_main.png)
+
+
+## Work with connectivity data
+In the connectivity panel, under selected dataset, you can find the source region
+    [![](images/connectivity_source_region.png)](images/connectivity_source_region.png)
+
+
+### Explore/change dataset
+From connectivity panel, you can change dataset or explore the description of the current dataset
+
+   [![](images/see_dataset_connectivity.png)](images/see_dataset_connectivity.png)
+   
+Hover on (i) info icon to display dataset description
+
+   [![](images/connectivity_dataset_description.png)](images/connectivity_dataset_description.png)
+   
+### Connected regions view
+At the top of the connectivity diagram, you can see two checkboxes: "Log10" and "All results"
+ 
+ 1. "Log10" checkbox is to see a diagram with logarithmic data. (Log10 checkbox is checked by default)
+ 
+  | Diagram with logarithmic data | Diagram without logarithmic data |
+  |-------------------------------|----------------------------------|
+  |    [![](images/con_diagram_log.png)](images/con_diagram_log.png) | [![](images/con_diagram_no_log.png)](images/con_diagram_no_log.png) |
+
+2. To see a number of connections on each connected region, the cursor should hover the desired area. 
+"All results" checkbox, displays connection number of all connected areas at once (Checkbox is unchecked by default)
+  
+  | Diagram with disabled "All results" | Diagram with enabled "All results" |
+  |-------------------------------|----------------------------------|
+  | [![](images/conn_disabled_all.png)](images/conn_disabled_all.png) | [![](images/conn_enabled_all.png)](images/conn_enabled_all.png) |
+
+By clicking the connected region, special panel will be expanded.
+
+ [![](images/conn_expanded_area.png)](images/conn_expanded_area.png)
+ 
+At the panel you can find a full name of the connected area and two buttons:
+ "Navigate" - to change template navigation and move to region.
+ "Connectivity" - to set region as source region and explore connectivity of it.
+
+
+
+## Export connectivity data
+At the end of the connectivity panel, you can find export buttons. 
+
+   [![](images/conn_export.png)](images/conn_export.png)
+
+
+You can export connectivity data with two options
+
+1. Export data as a CSV file
+2. Export data as "png" format image
+
+## Close Connectivity
+You can close connectivity from a close button on the top right side of the connectivity section at the right-side panel.
+
+   [![](images/close_connectivity.png)](images/close_connectivity.png)
+
+
+1. After clicking the close button, the standard parcellation region color map will be returned to the viewer. 
+2. Connectivity data will be disappeared from a side panel
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mkdocs.yml

@@ -21,6 +21,7 @@ pages:
     - Selecting: 'usage/selecting.md'
     - Navigating: 'usage/navigating.md'
     - Searching: 'usage/search.md'
+    - Connectivity: 'usage/connectivity.md'
   - Advanced usage:
     - Keyboard shortcuts: 'advanced/keyboard.md'
     - URL parsing: 'advanced/url.md'