From 41aa553469fc6b3a135515149eaae7e3212f83f7 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Wed, 18 Mar 2020 14:31:42 +0100
Subject: [PATCH] chore: small fixes
---
docs/usage/connectivity.md | 109 +++++++++++++++++--------------------
mkdocs.yml | 2 +-
2 files changed, 50 insertions(+), 61 deletions(-)
diff --git a/docs/usage/connectivity.md b/docs/usage/connectivity.md
index e84b820f0..e3381d9f3 100644
--- a/docs/usage/connectivity.md
+++ b/docs/usage/connectivity.md
@@ -1,92 +1,81 @@
-# Connectivity matrix
+# Exploring connectivity
-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.
+The interactive atlas viewer allows the exploration of connectivity of parcellation regions, based on datasets curated in 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.
+Currently, connectivity data is explorable for the parcellation `JuBrain Cytoarchitectonic Atlas`, which is available in template spaces `MNI Colin 27` and `ICBM 2009c Nonlinear Asymmetric`.
-## Explore area connectivity
-Select parcellation "JuBrain Cytoarchitectonic Atlas" and click on a region to bring up a context-specific menu
+## Getting started
-[](images/region_menu_with_connectivity.png)
+- Select parcellation `JuBrain Cytoarchitectonic Atlas` and click on a region to bring up a context-specific menu
-By clicking on the "Connectivity" button, available datasets for connectivity will be displayed
+ [](images/region_menu_with_connectivity.png)
-[](images/connectivity_dataset_menu.png)
+- Click the `Connectivity` button, available datasets for connectivity will be displayed
-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:
+ [](images/connectivity_dataset_menu.png)
-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)
-
- - Color map after selecting connectivity
+- Click on a dataset (e.g. `1000 Brain Study - DTI connectivity`) to explore the connectivity data associated with it.
+
+## Working with connectivity data
+
+Upon selecting a preview dataset, several aspects of the UI will change:
+
+- the color map of the parcellation will be replaced by a heat map, derived from the magnitutde of connectivity.
+
+ | Regular color map | Connectivity heat map |
+ | --- | --- |
+ | [](images/connectivity_color_before.png) | [](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
+- a side panel will be opened, showing the tabulated data of the connectivity.
[](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)
+### Tabulated side panel
+
+In the tabulated view, the selected dataset can be reviewed and changed.
+
+[](images/see_dataset_connectivity.png)
+[](images/connectivity_dataset_description.png)
-### Explore/change dataset
-From connectivity panel, you can change dataset or explore the description of the current dataset
+The source region is displayed in the tabulated view.
- [](images/see_dataset_connectivity.png)
-
-Hover on (i) info icon to display dataset description
+[](images/connectivity_source_region.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_no_log.png) |
+The magnitude of the connectivity can either be displayed linearly or logarithmically by toggling the `Log10` checkbox.
-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_enabled_all.png) |
+| Connectivity plotted logarithmically `default` | Connectivity plotted linearly |
+| --- | --- |
+| [](images/con_diagram_log.png) | [](images/con_diagram_no_log.png) |
-By clicking the connected region, special panel will be expanded.
+The display of magnitude of the connectivity can also be toggled with `All results` checkbox.
- [](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.
+| Hiding magnitude `default` | Showing magnitude |
+| --- | --- |
+| [](images/conn_disabled_all.png) | [](images/conn_enabled_all.png) |
+Clicking on any of the connected region will reveal a region context menu. In addition to the full name of the region, two buttons are present:
+- `Navigate` - navigate to the region of interest.
+- `Connectivity` - to the region of interest as the source, and explore its connectivity with other parcellation regions.
-## Export connectivity data
-At the end of the connectivity panel, you can find export buttons.
+[](images/conn_expanded_area.png)
- [](images/conn_export.png)
+### Export
+At the bottom of the side panel, `export` buttons can be found. The data can either be exported as a CSV or PNG.
-You can export connectivity data with two options
+[](images/conn_export.png)
-1. Export data as a CSV file
-2. Export data as "png" format image
+## Exit
-## Close Connectivity
-You can close connectivity from a close button on the top right side of the connectivity section at the right-side panel.
+To exit the connectivity mode, click the close button located at the top right side of the side panel.
- [](images/close_connectivity.png)
+[](images/close_connectivity.png)
+Exiting the connectivity mode will:
-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
\ No newline at end of file
+- restore the colour map of the parcellation
+- remove the connectivity side panel
diff --git a/mkdocs.yml b/mkdocs.yml
index 0b5b218f4..ccd849296 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -21,7 +21,7 @@ pages:
- Selecting: 'usage/selecting.md'
- Navigating: 'usage/navigating.md'
- Searching: 'usage/search.md'
- - Connectivity: 'usage/connectivity.md'
+ - Exploring connectivity: 'usage/connectivity.md'
- Advanced usage:
- Keyboard shortcuts: 'advanced/keyboard.md'
- URL parsing: 'advanced/url.md'
--
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