Adjust default bigdata

[alexvpickering]

Description

This pull request introduces cell-count-aware default configurations for embedding plots, particularly optimizing marker settings for large datasets (over 100,000 cells). It does so by dynamically adjusting plot defaults and reset behavior based on the number of cells, ensuring better performance and clarity in visualizations with large data. The changes also standardize how initial plot configurations are determined and compared, and introduce a new utility for handling these adjustments.

Cell-count-aware embedding plot configuration:

• Added a new utility, getEmbeddingInitialConfig, which returns the initial config for embedding plots, adjusting marker size and outline for datasets with more than 100,000 cells. Also added helpers getTotalCellCount and isEmbeddingPlotType for cell count calculations and plot type checks (src/utils/plotConfig/getEmbeddingInitialConfig.js).
• Updated embedding plot components (ConfigureEmbedding, DataIntegration, PlotContainer) to use getEmbeddingInitialConfig for setting initial config, reset logic, and to auto-apply large-dataset marker defaults if the config hasn't been customized by the user (src/components/data-processing/ConfigureEmbedding/ConfigureEmbedding.jsx, src/components/data-processing/DataIntegration/DataIntegration.jsx, src/components/plots/PlotContainer.jsx). [1] [2] [3]

Reset and config comparison improvements:

• Modified config comparison logic in all relevant components to skip defaultValues (which is now used for metadata about defaults), ensuring accurate detection of user-customized settings and correct enabling/disabling of the reset button (src/components/data-processing/ConfigureEmbedding/ConfigureEmbedding.jsx, src/components/data-processing/DataIntegration/DataIntegration.jsx, src/components/plots/PlotLayout.jsx, src/components/plots/PlotContainer.jsx). [1] [2] [3] [4]
• Updated reset logic to use the cell-count-aware initial config for embedding plots, preserving fields marked as keepValuesOnReset where appropriate (src/components/data-processing/ConfigureEmbedding/ConfigureEmbedding.jsx, src/components/data-processing/DataIntegration/DataIntegration.jsx, src/components/plots/PlotContainer.jsx). [1] [2] [3]

Initial state adjustments:

• Set the color gradient to 'spectral' by default for several embedding preview plot initial configs, improving visual consistency for mitochondrial content, doublet score, number of genes, and number of UMIs (src/redux/reducers/componentConfig/initialState.js). [1] [2] [3] [4]

Details

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Integration test branch

master

Merge checklist

Your changes will be ready for merging after all of the steps below have been completed.

Code updates

Have best practices and ongoing refactors being observed in this PR

• Migrated any selector / reducer used to the new format.
• All new dependency licenses have been checked for compatibility.

Manual/unit testing

• Tested changes using InfraMock locally or no tests required for change, e.g. Kubernetes chart updates.
• Validated that current unit tests for code work as expected and are sufficient for code coverage or no unit tests required for change, e.g. documentation update.
• Unit tests written or no unit tests required for change, e.g. documentation update.

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• Started end-to-end tests on the latest commit.

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• Relevant Github READMEs updated or no GitHub README updates required.
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Optional

• Staging environment is unstaged before merging.
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[dbmi-svc-checkmarx]

Checkmarx One – Scan Summary & Details – 95d60acb-0e49-4dfa-a383-3fe16e27781f

Great job! No new security vulnerabilities introduced in this pull request

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[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	684.87 KB (🟡 +11 B)

Details

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Twelve Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/experiments/[experimentId]/data-processing	490.61 KB (🟡 +589 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/dot-plot	445.79 KB (🟡 +709 B)	1.1 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical	446.33 KB (🟡 +687 B)	1.1 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous	466.63 KB (🟡 +709 B)	1.12 MB
/experiments/[experimentId]/plots-and-tables/frequency	447.61 KB (🟡 +671 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap	535.99 KB (🟡 +710 B)	1.19 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix	140.21 KB (🟡 +694 B)	825.08 KB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	893.71 KB (🟡 +710 B)	1.54 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	895.56 KB (🟡 +711 B)	1.54 MB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis	449.49 KB (🟡 +687 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/violin	467.74 KB (🟡 +710 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/volcano	452.08 KB (🟡 +705 B)	1.11 MB

Details

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