diff --git a/docs/_config.yml b/docs/_config.yml index 98c782ea..cb208850 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -3,8 +3,8 @@ title: cOmicsART Documentation logo: "/assets/images/Logo_cOmicsArt.svg" # Update to the new image file path description: Here you find all the information you need to use cOmicsART -#theme: just-the-docs -remote_theme: just-the-docs/just-the-docs +theme: just-the-docs +#remote_theme: just-the-docs/just-the-docs # Include custom CSS just_the_docs: diff --git a/docs/_site/assets/js/search-data.json b/docs/_site/assets/js/search-data.json index c983161b..d935c68b 100644 --- a/docs/_site/assets/js/search-data.json +++ b/docs/_site/assets/js/search-data.json @@ -49,11 +49,11 @@ "relUrl": "/interface-details/heatmap.html" },"7": { "doc": "Welcome to cOmicsART", - "title": "Welcome to cOmicsArt Documentation 🎨", + "title": "Welcome to cOmicsArt Documentation 🎨", "content": "If you are looking for the web app, please visit: 🌐 cOmicsART Web App . Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section. Have fun exploring! πŸŽ‰ . Quick Links to Get You Started: . | πŸ“š Want to know the required data and format? Visit Interface Details. | πŸ”§ Need to run the app locally? Check out the Installation Guide. | πŸ’‘ Looking for customization inspiration? Explore our Customization Examples. | πŸ“Š Want to know more about the significance analysis? Visit Significance Analysis | . ", - "url": "/#welcome-to---comicsart-documentation-", + "url": "/#welcome-to----comicsart-documentation-", - "relUrl": "/#welcome-to---comicsart-documentation-" + "relUrl": "/#welcome-to----comicsart-documentation-" },"8": { "doc": "Welcome to cOmicsART", "title": "Welcome to cOmicsART", @@ -106,17 +106,17 @@ },"15": { "doc": "Interface Details", "title": "Interface Details", - "content": "If you need tab specific information navigate to the respective documentation using the left sidebar. ", + "content": "If you need tab-specific information, navigate to the respective documentation using the left sidebar. ", "url": "/interface-details.html", "relUrl": "/interface-details.html" },"16": { "doc": "Interface Details", - "title": "General Details about the interface.", - "content": ". | general design choices | when to press a button | what are buttons, tabs | dependencies of the tabs | . ", - "url": "/interface-details.html#general-details-about-the-interface", + "title": "General Design Characteristics", + "content": "User Interface and Analysis Features . The cOmicsART user interface evolves gradually to guide users through the necessary steps: . | Data Input Tab: The initial tab where users upload their data. A successful data upload is necessary before accessing the next tab. | Pre-Processing Tab: This tab becomes accessible after a successful data upload. It offers multiple options to prepare the data for analysis, including diagnostic plots to check for normal distribution. | Analysis Tabs: Six analysis options are available, each in its own tab. These tabs provide interactive result visualizations and various analytical functions. | . To get more information on the tabs, navigate to the respective documentation using the left sidebar. Navigation Principles . | Button Clicks: Used to evoke actions. | Loading Bars: Display waiting times during processing. | Question Marks: Provide quick help and guide to respective detailed documentation found on this very site | Dropdown Menus: Offer options for selection. Sometime multiple items can be selected. If clicking on a selected item it is removed from the selection | Checkboxes: If a checkbox is clicked, the respective feature is activated. If clicked again, the feature is deactivated. | Sliding Bars: Used to adjust numeric parameters or ranges. The range of the sliding bar is displayed above the bar. Simply slide the bar to the desired value. | Text Fields: Used to enter text. Within cOmicsART these fields are mostly used to hold your Notes, which are saved in the HTML report at approporiate position. You can use markdown syntax here. | . Features Across Tabs . | Side Panel Structure: Each tab, except the input tab, has a side panel divided by a horizontal line: . | Upper Section: Contains options affecting the analysis, requiring recomputation when changed. The analysis is triggered by a \"Do/Get analysis\" button above the division line. | Lower Section: Displays secondary parameters with changes reflecting immediately in the results (automatic update). | . | Download Options: Users can download autogenerated, HTML reports as well as visualizations and results in common formats (e.g., PNG, XLSX). There are respective buttons. | . ", + "url": "/interface-details.html#general-design-characteristics", - "relUrl": "/interface-details.html#general-details-about-the-interface" + "relUrl": "/interface-details.html#general-design-characteristics" },"17": { "doc": "PCA", "title": "PCA", @@ -217,11 +217,11 @@ "relUrl": "/interface-details/single-gene-visualisations.html" },"31": { "doc": "Welcome to cOmicsART", - "title": "Welcome to cOmicsArt Documentation 🎨", + "title": "Welcome to cOmicsArt Documentation 🎨", "content": "If you are looking for the web app, please visit: 🌐 cOmicsART Web App . Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section. Have fun exploring! πŸŽ‰ . Quick Links to Get You Started: . | πŸ“š Want to know the required data and format? Visit Interface Details. | πŸ”§ Need to run the app locally? Check out the Installation Guide. | πŸ’‘ Looking for customization inspiration? Explore our Customization Examples. | πŸ“Š Want to know more about the significance analysis? Visit Significance Analysis | . ", - "url": "/welcome.html#welcome-to---comicsart-documentation-", + "url": "/welcome.html#welcome-to--comicsart-documentation-", - "relUrl": "/welcome.html#welcome-to---comicsart-documentation-" + "relUrl": "/welcome.html#welcome-to--comicsart-documentation-" },"32": { "doc": "Welcome to cOmicsART", "title": "Welcome to cOmicsART", diff --git a/docs/_site/index.html b/docs/_site/index.html index 44f56771..708c127f 100644 --- a/docs/_site/index.html +++ b/docs/_site/index.html @@ -1 +1 @@ - Welcome to cOmicsART | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied

Welcome to cOmicsArt Documentation 🎨

If you are looking for the web app, please visit: 🌐 cOmicsART Web App

Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section.

Have fun exploring! πŸŽ‰

+ Welcome to cOmicsART | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied

Welcome to cOmicsArt Documentation 🎨

If you are looking for the web app, please visit: 🌐 cOmicsART Web App

Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section.

Have fun exploring! πŸŽ‰

diff --git a/docs/_site/interface-details.html b/docs/_site/interface-details.html index f88d54f8..e2cae4a7 100644 --- a/docs/_site/interface-details.html +++ b/docs/_site/interface-details.html @@ -1 +1 @@ - Interface Details | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied

Interface Details

If you need tab specific information navigate to the respective documentation using the left sidebar.

General Details about the interface.

  • general design choices
  • when to press a button
  • what are buttons, tabs
  • dependencies of the tabs

Table of contents

+ Interface Details | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied

Interface Details

If you need tab-specific information, navigate to the respective documentation using the left sidebar.

General Design Characteristics

User Interface and Analysis Features

The cOmicsART user interface evolves gradually to guide users through the necessary steps:

  • Data Input Tab: The initial tab where users upload their data. A successful data upload is necessary before accessing the next tab.
  • Pre-Processing Tab: This tab becomes accessible after a successful data upload. It offers multiple options to prepare the data for analysis, including diagnostic plots to check for normal distribution.
  • Analysis Tabs: Six analysis options are available, each in its own tab. These tabs provide interactive result visualizations and various analytical functions.

To get more information on the tabs, navigate to the respective documentation using the left sidebar.

  • Button Clicks: Used to evoke actions.
  • Loading Bars: Display waiting times during processing.
  • Question Marks: Provide quick help and guide to respective detailed documentation found on this very site
  • Dropdown Menus: Offer options for selection. Sometime multiple items can be selected. If clicking on a selected item it is removed from the selection
  • Checkboxes: If a checkbox is clicked, the respective feature is activated. If clicked again, the feature is deactivated.
  • Sliding Bars: Used to adjust numeric parameters or ranges. The range of the sliding bar is displayed above the bar. Simply slide the bar to the desired value.
  • Text Fields: Used to enter text. Within cOmicsART these fields are mostly used to hold your Notes, which are saved in the HTML report at approporiate position. You can use markdown syntax here.

Features Across Tabs

  1. Side Panel Structure: Each tab, except the input tab, has a side panel divided by a horizontal line:
    • Upper Section: Contains options affecting the analysis, requiring recomputation when changed. The analysis is triggered by a "Do/Get analysis" button above the division line.
    • Lower Section: Displays secondary parameters with changes reflecting immediately in the results (automatic update).
  2. Download Options: Users can download autogenerated, HTML reports as well as visualizations and results in common formats (e.g., PNG, XLSX). There are respective buttons.
The design of the sidepanel

Table of contents

diff --git a/docs/_site/welcome.html b/docs/_site/welcome.html index 6d1b7490..ece4220e 100644 --- a/docs/_site/welcome.html +++ b/docs/_site/welcome.html @@ -1 +1 @@ - Welcome to cOmicsART | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied

Welcome to cOmicsArt Documentation 🎨

If you are looking for the web app, please visit: 🌐 cOmicsART Web App

Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section.

Have fun exploring! πŸŽ‰

+ Welcome to cOmicsART | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied

Welcome to cOmicsArt Documentation 🎨

If you are looking for the web app, please visit: 🌐 cOmicsART Web App

Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section.

Have fun exploring! πŸŽ‰

diff --git a/docs/index.md b/docs/index.md index c49542e9..49abead4 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,7 +4,7 @@ layout: default nav_exclude: true --- -# Welcome to cOmicsArt Documentation 🎨 +# Welcome to cOmicsArt Documentation 🎨 If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://comicsart.org/) diff --git a/docs/interface-details.md b/docs/interface-details.md index ac0e53a9..d277f54a 100644 --- a/docs/interface-details.md +++ b/docs/interface-details.md @@ -6,9 +6,50 @@ nav_order: 2 --- # Interface Details -If you need tab specific information navigate to the respective documentation using the left sidebar. -## General Details about the interface. -- general design choices -- when to press a button -- what are buttons, tabs -- dependencies of the tabs + +If you need tab-specific information, navigate to the respective documentation using the left sidebar. + +## General Design Characteristics + +### User Interface and Analysis Features + +The cOmicsART user interface evolves gradually to guide users through the necessary steps: + +- **Data Input Tab**: The initial tab where users upload their data. A successful data upload is necessary before accessing the next tab. +- **Pre-Processing Tab**: This tab becomes accessible after a successful data upload. It offers multiple options to prepare the data for analysis, including diagnostic plots to check for normal distribution. +- **Analysis Tabs**: Six analysis options are available, each in its own tab. These tabs provide interactive result visualizations and various analytical functions. + +To get more information on the tabs, navigate to the respective documentation using the left sidebar. + + +### Navigation Principles + +- **Button Clicks**: Used to evoke actions. +- **Loading Bars**: Display waiting times during processing. +- **Question Marks**: Provide quick help and guide to respective detailed documentation found on this very site +- **Dropdown Menus**: Offer options for selection. Sometime multiple items can be selected. If clicking on a selected item it is removed from the selection +- **Checkboxes**: If a checkbox is clicked, the respective feature is activated. If clicked again, the feature is deactivated. +- **Sliding Bars**: Used to adjust numeric parameters or ranges. The range of the sliding bar is displayed above the bar. Simply slide the bar to the desired value. +- **Text Fields**: Used to enter text. Within cOmicsART these fields are mostly used to hold your Notes, which are saved in the HTML report at approporiate position. You can use [markdown syntax](https://www.markdownguide.org/cheat-sheet/) here. + + +### Features Across Tabs +
+
+
    +
  1. Side Panel Structure: Each tab, except the input tab, has a side panel divided by a horizontal line: +
      +
    • Upper Section: Contains options affecting the analysis, requiring recomputation when changed. The analysis is triggered by a "Do/Get analysis" button above the division line.
      • +
    • Lower Section: Displays secondary parameters with changes reflecting immediately in the results (automatic update).
      • +
    +
    2. +
  2. Download Options: Users can download autogenerated, HTML reports as well as visualizations and results in common formats (e.g., PNG, XLSX). There are respective buttons. +
    3. +
+
+
+ The design of the sidepanel +
+ + + diff --git a/docs/welcome.md b/docs/welcome.md index 377fa0fd..a591a872 100644 --- a/docs/welcome.md +++ b/docs/welcome.md @@ -4,13 +4,13 @@ layout: default nav_order: 1 --- -# Welcome to cOmicsArt Documentation 🎨 +# Welcome to cOmicsArt Documentation 🎨 If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://comicsart.org/) Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section. -Have fun exploring! πŸŽ‰ +**Have fun exploring!** πŸŽ‰ ### Quick Links to Get You Started: