Pull request for altexp functionality

[ArioMoniri]

🧪 Multiple Experimental Assay Analysis Tool

🚀 Updates & Additions

✅ UI Enhancements:

• Added new components to the User Interface (UI).
• Some UI elements might be unnecessary and could be removed.

✅ Core Functionality:

• Updated Main Function with improvements.
• Made changes to Utils to support additional features.

✅ CI/CD Improvements:

• Integrated CI/CD pipeline updates.

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⚠️ Issues & Solutions

🔗 Issue: Microbiome Analysis Dashboard Header Redirection

• The header of Microbiome Analysis Dashboard - v0.99.7 redirected to the main page, but did not refresh the page.

✅ Solution:

• Added a force refresh to the onClick redirection in the miaDash file.

🔍 Effect:

• Ensures that the page reloads properly when clicking on the header.

🛠️ Issue: Large Dataset Handling

• The package struggles with handling large datasets, but no edits were made for this yet.

🚨 Next Steps:

• Investigate and implement data size checker and custom default panels list for large datasets.

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📉 Visualization & UI Concerns

❗ Alternative Expression (Alt Exp) Plot Visualization

• Issue: Haven't been able to fully test Alt Exp visualization because no dummy data is available in a merged RDS format.
• Need to validate:
  • 📊 Plot visualization logic
  • 📂 Dropdown menu functionality for selecting agglomeration or visualization method

💡 Solution Needed:

• Dummy Data Required 📝🔬 (Merged .rds format for proper testing).

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🔧 Next Steps

🔍 Review & Cleanup:

• Identify and remove unnecessary UI elements.

🛠 Debugging & Testing:

• Validate plot visualization & dropdown selection.
• Create & test with dummy merged .rds data.

⚡ Optimize Large Dataset Handling:

• Address the package issue affecting large dataset performance.

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[ArioMoniri]

let see ( in some parts it didnt pass the codeFactor but they are not sth effecting the plot generation

[RiboRings]

Thanks a lot for the additions and fixes. Let's begin with the altExp functionality.

We don't expect the users to import altExp by themselves. It is more likely that they want to create altExps when subsetting or agglomerating the TreeSE without replacing the original experiment. So we could:

• Remove Alternative Experiment tab in Import box
• Add a new tab called for instance "Switch" to the Manipulate box, which allows users to switch from an experiment to another for all the future operations. I think there is a slot in TreeSE objects called mainExpName that might be useful for this.
• Remove "Apply to" from the Manipulate box
• Add a checkbox to Subset and Agglomerate tabs so users can select if they want to replace the current TreeSE or store the new object as an altExp, and if so under which name. These two elements (checkbox and text box for naming) can be shared by the two tabs), check how it's done for example in alpha and beta diversity naming box.

For the new parameters in the Visualise box, I think they are doing the same as the Panels list below(?)

Thanks again! I'll check the rest after we get through these initial changes. I'm open for further discussion if needed!