Merge pull request #52 from plantinformatics/develop

Release 18/12

.github/workflows/repo__auto-update-param-branch.yml → .github/workflows/repo__manual-reset-param-branch.yml

@@ -1,22 +1,19 @@
-name: repo__auto-update-param-branch
+name: repo__manual-reset-param-branch
 
 on:
-  push:
-    branches:
-      - main # Trigger on pushes to main branch
   workflow_dispatch:  # Allow manual triggering
 
 jobs:
-  auto-merge:
+  reset:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
-      - name: Merge develop -> test-space/pk
+      - name: Reset test-space/pk to develop
         run: |
           git config user.name github-actions
           git config user.email [email protected]
-          git checkout develop
-          git rebase origin/develop
-          git push --force-with-lease origin develop
+          git checkout test-space/pk
+          git reset --hard origin/develop
+          git push --force-with-lease origin test-space/pk

docs/Basic-Functions/Axis-Title-menu-layout.md

@@ -0,0 +1,83 @@
+# Axis Title menu layout
+Click on the axis title to open the Axis Title menu. This offers several functionalities, as shown below, enabling users to visualize data in a way that best aligns with their objectives.
+
+![Axis Title Menu Updated- final](https://github.com/user-attachments/assets/c39d9534-34c1-406c-ac6a-1d268d846cea)
+
+## Split Axis
+To view multiple data sets simultaneously, such as different marker types or genes aligned against the same genome or chromosome, the split axis feature is very useful. To enable it, click on the axis menu layout, select the downward-slanting arrow, and close the menu by clicking the cross in the top right corner.
+
+Split axis could be done either before or after adding datasets to the axis.
+
+![2a-split-axis](https://github.com/user-attachments/assets/26e7b4a8-b6e3-42f1-a8c3-c9110efe06ac)
+
+### Zooming the axis
+
+Upon zooming in the axis (Click and drag) the representation of individual features transitions from a histogram to a more distinct fingerprint view.
+
+![2b-split-axis-zoom-in](https://github.com/user-attachments/assets/9a4f931e-5cda-450f-92c6-75f93d4ba1e7)
+
+### Viewing the features 
+
+=== "Adding Feature"
+
+    Selecting an individual fingerprint band allows the user to view the feature's location, represented by an arrow, and selecting the arrow displays the feature name. 
+
+    ![2c-split-axis-add-feature](https://github.com/user-attachments/assets/30f19a38-cc6c-4792-9f6f-bf568122ef2a)
+     
+=== "Hiding Feature"
+
+    Clicking the feature arrow hides the feature name, and selecting the fingerprint band again hides the feature entirely.
+
+    ![2d-split-axis-remove-feature](https://github.com/user-attachments/assets/2cc78f74-0d63-4d5c-890a-b344e8c9456c)
+
+!!!note
+  Deselect any displayed feature to ensure it is not automatically displayed the next time the same dataset is opened.
+
+## Flip Axis
+
+To flip or invert the axis, open the Axis Title menu and select the icon with up and down pointing arrows. See the image below for a visual representation.
+
+![3-flip-axis](https://github.com/user-attachments/assets/d617c796-1ab5-4382-a063-66d9861ca70f)
+
+![basic-function_axis-flip-orientation](https://github.com/user-attachments/assets/2bd66224-a23e-47e0-8c18-5aeeb9ec6e3a)
+
+## Removing Datasets from visualization
+
+=== "Specific Dataset"
+
+    Open the Axis Title menu and click the cross icon next to a specific dataset to remove it from the displayed view.
+
+    ![5a  remove selected dataset](https://github.com/user-attachments/assets/ec022dd1-6f93-4448-b89c-bb2c86b46f54)
+
+       
+=== "All Datasets"
+
+    To remove all datasets from view, open the Axis Title menu and click the cross icon located above the axis name.
+
+    ![5b  Removing all datasets](https://github.com/user-attachments/assets/038e5990-b8cd-4e99-bbf3-32903739f647)
+
+## Rename Axis title
+
+To rename the axis title, open the Axis Title menu and click the pen icon to access the text bar. Enter a new axis title that aligns with your objective.
+
+![4 rename](https://github.com/user-attachments/assets/62495c11-99c1-4f73-b101-c3e2a47e258a)
+
+## Display and hide features of a dataset
+
+Open the Axis Title menu and click the eye icon to toggle the display of a particular dataset, showing or hiding it from view.
+
+=== "Display feature"
+
+    ![6a-hide-features](https://github.com/user-attachments/assets/e0d58454-09b0-4466-b51b-db4d98df0c65)
+
+=== "Hide feature"
+
+    ![6b-display-features](https://github.com/user-attachments/assets/a123b35a-f335-4cbb-832d-6b119734e6e2)
+
+## Requested features vs total features of a dataset
+
+!!!note
+    This is an advanced feature used to debug technical issues with Pretzel. It is a technical counter that tracks the number of features requested from the backend.
+
+![7Requested feature vs total feature](https://github.com/user-attachments/assets/d70269f6-bdb3-41d1-a595-2498ee66bafb)
+