Bugfix : Correctly overlay Chromatogram plots over each other if multiple options are selected

[subCode321]

Fixes #230

Now, I am collecting all the dataframes in a list in order to aggregate them, so that the chromatograms can be shown together.

Here's the recording for the same

Untitled.video.-.Made.with.Clipchamp.10.mp4

Summary by CodeRabbit

• New Features

  • Overlaid chromatogram plots now integrate TIC, BPC, and optionally XIC for a more comprehensive visualization.

• Enhancements

  • Improved data aggregation ensures duplicate entries are correctly consolidated.
  • Enhanced user notifications alert when no chromatogram data is available for plotting.

[coderabbitai]

Walkthrough

The function plot_bpc_tic has been refactored to enhance chromatogram plotting. It now aggregates data for TIC, BPC, and optionally XIC/EIC by grouping and summing duplicate retention time entries. The plotting process is streamlined using a list to collect DataFrames before concatenation and plotting. Additionally, error handling for cases with no available chromatogram data has been introduced, along with adjustments in the layout update mechanics, as documented in the updated function docstring.

Changes

File	Change Summary
src/view.py	Updated plot_bpc_tic docstring; refactored plotting logic to use a DataFrame list for TIC, BPC, and optionally XIC/EIC; aggregates duplicate RT entries; added error handling; moved template assignment to a separate layout update method.

Sequence Diagram(s)

sequenceDiagram
    participant U as User
    participant F as plot_bpc_tic
    participant DA as Data Aggregator
    participant PG as Plot Generator

    U ->> F: Call plot_bpc_tic()
    F ->> DA: Group & aggregate TIC data
    DA -->> F: Return TIC DataFrame
    F ->> DA: Group & aggregate BPC data
    DA -->> F: Return BPC DataFrame
    F ->> DA: Optionally process XIC/EIC (sum duplicate RTs)
    DA -->> F: Return XIC/EIC DataFrame
    F ->> F: Check for available chromatogram data
    alt Data available
        F ->> PG: Concatenate and sort DataFrames
        PG -->> F: Overlaid chromatogram figure
        F -->> U: Return figure with updated layout
    else No data
        F -->> U: Error message: No chromatogram data available
    end

Loading

Assessment against linked issues

Objective	Addressed	Explanation
Overlay of chromatograms with multiple selections (#230)	✅

Poem

In the code garden, I hop with cheer,
Chromatograms join in a dance so clear.
Data frames prance and neatly align,
Bugs vanish as the plots combine.
With a twitch of my nose and a joyful leap,
I sing of clean code that makes hearts leap! 🐇

---

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📥 Commits

Reviewing files that changed from the base of the PR and between 3352c27 and 4114eb8.

📒 Files selected for processing (1)

• src/view.py (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (4)

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🔇 Additional comments (10)

src/view.py (10)

67-72: Clear docstring update to reflect enhanced functionality

The docstring has been properly updated to indicate that the function now plots TIC, BPC, and optionally XIC, with all chromatograms overlaid. This clarification accurately describes the improved functionality.

---

73-75: Good design approach for aggregating chromatogram data

Creating a list to store DataFrames for each chromatogram type is an excellent solution for the overlay issue. This approach allows all chromatograms to be concatenated before plotting, ensuring they display correctly in a single figure.

---

79-83: Clean implementation of TIC data preparation

The TIC DataFrame creation now properly groups and sums data, adds a type identifier, tracks the maximum intensity, and stores the result in the collection list rather than plotting immediately. This is key to solving the overlay issue.

---

86-90: Clean implementation of BPC data preparation

Similar to the TIC implementation, the BPC DataFrame is now correctly prepared by grouping by retention time and taking the maximum intensity at each point. Adding it to the collection list enables proper overlay in the final plot.

---

94-113: Improved XIC/EIC data handling with proper aggregation

The XIC implementation now includes proper input sanitization with comma-to-period conversion and adds crucial aggregation of duplicate retention time entries by summing intensities. This ensures XIC data is correctly prepared for overlay with other chromatograms.

---

116-118: Good error handling for empty data scenarios

Adding a check for empty data with appropriate user feedback is an excellent defensive programming practice. This prevents potential errors or blank plots when no chromatogram data is available.

---

120-124: Well-structured data preparation for visualization

The DataFrame concatenation followed by categorical type conversion and sorting ensures consistent ordering of chromatograms in the plot. This provides a predictable visual representation for users.

---

126-127: Good use of consistent color mapping

Defining a specific color map for each chromatogram type ensures visual consistency and makes it easier for users to distinguish between different data series in the overlay.

---

129-139: Clean implementation of unified plotting

The plot creation now correctly uses the combined DataFrame with appropriate parameters, including the crucial by="type" parameter that enables proper overlay of the different chromatogram types.

---

148-148: Cleaner template implementation

Moving the template specification to the update_layout method is a cleaner approach than directly modifying the figure's layout property.

✨ Finishing Touches

• 📝 Generate Docstrings

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[subCode321]

@t0mdavid-m , kindly check