From 00c5004c27859183de94b6f96ee65017ea22f5a1 Mon Sep 17 00:00:00 2001 From: pk0t Date: Fri, 29 Nov 2024 11:20:54 +1100 Subject: [PATCH 1/3] Create Axis-Title-menu-layout.md Adding documentation for Axis title menu --- docs/Axis-Title-menu-layout.md | 81 ++++++++++++++++++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 docs/Axis-Title-menu-layout.md diff --git a/docs/Axis-Title-menu-layout.md b/docs/Axis-Title-menu-layout.md new file mode 100644 index 0000000..776e315 --- /dev/null +++ b/docs/Axis-Title-menu-layout.md @@ -0,0 +1,81 @@ +# 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 Layout- final](https://github.com/user-attachments/assets/f4853b09-806a-451b-845b-d89acdfbc495) + +## Split Axis +To view multiple data sets simultaneously, such as different marker types or genes aligned against the same genome or chromosome, the axis-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. For instance, + +![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 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) + +## Selected features vs total features of a dataset + +When zooming in on a specific genomic segment, the Axis Title menu displays the number of features within the selected region relative to the total features on the chromosome. + +![7 Selected and total features](https://github.com/user-attachments/assets/b712a1bc-c69a-4ae7-bff5-800ec4b5a37f) From 4f8d894d2e8bafab5f65e8ff8746e22d8cafcfdc Mon Sep 17 00:00:00 2001 From: pk0t Date: Tue, 10 Dec 2024 12:10:31 +1100 Subject: [PATCH 2/3] Update Axis-Title-menu-layout.md --- docs/Axis-Title-menu-layout.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/Axis-Title-menu-layout.md b/docs/Axis-Title-menu-layout.md index 776e315..b3e125c 100644 --- a/docs/Axis-Title-menu-layout.md +++ b/docs/Axis-Title-menu-layout.md @@ -1,7 +1,7 @@ # 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 Layout- final](https://github.com/user-attachments/assets/f4853b09-806a-451b-845b-d89acdfbc495) +![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 axis-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. @@ -74,8 +74,10 @@ Open the Axis Title menu and click the eye icon to toggle the display of a parti ![6b-display-features](https://github.com/user-attachments/assets/a123b35a-f335-4cbb-832d-6b119734e6e2) -## Selected features vs total features of a dataset +## Requested features vs total features of a dataset -When zooming in on a specific genomic segment, the Axis Title menu displays the number of features within the selected region relative to the total features on the chromosome. +!!!note + This is an advanced feature used to debug technical issues with Pretzel. It is a technical counter taht 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) -![7 Selected and total features](https://github.com/user-attachments/assets/b712a1bc-c69a-4ae7-bff5-800ec4b5a37f) From 16af2f3395b0415c2ec31218feec025d6fae575b Mon Sep 17 00:00:00 2001 From: kennyAgricultureVic Date: Tue, 10 Dec 2024 12:25:01 +1100 Subject: [PATCH 3/3] Fix file location error and fixed up minor grammatical and spelling errors --- docs/{ => Basic-Functions}/Axis-Title-menu-layout.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename docs/{ => Basic-Functions}/Axis-Title-menu-layout.md (87%) diff --git a/docs/Axis-Title-menu-layout.md b/docs/Basic-Functions/Axis-Title-menu-layout.md similarity index 87% rename from docs/Axis-Title-menu-layout.md rename to docs/Basic-Functions/Axis-Title-menu-layout.md index b3e125c..c59783e 100644 --- a/docs/Axis-Title-menu-layout.md +++ b/docs/Basic-Functions/Axis-Title-menu-layout.md @@ -4,7 +4,7 @@ Click on the axis title to open the Axis Title menu. This offers several functio ![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 axis-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. +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. @@ -20,7 +20,7 @@ Upon zooming in the axis (Click and drag) the representation of individual featu === "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. + 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) @@ -35,7 +35,7 @@ Upon zooming in the axis (Click and drag) the representation of individual featu ## Flip Axis -To flip or invert the axis, open the Axis Title menu and select the icon with up and down pointing arrows. For instance, +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) @@ -62,7 +62,7 @@ To rename the axis title, open the Axis Title menu and click the pen icon to acc ![4 rename](https://github.com/user-attachments/assets/62495c11-99c1-4f73-b101-c3e2a47e258a) -## Display and hide features of dataset +## 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. @@ -77,7 +77,7 @@ Open the Axis Title menu and click the eye icon to toggle the display of a parti ## 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 taht tracks the number of features requested from the backend. + 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)