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Fix ANOVA and pairwise gene set enrichment and spatial registration plot visualization - #125

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manishabarse wants to merge 2 commits into
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app_layer_colors
Open

manishabarse wants to merge 2 commits into
develfrom
app_layer_colors

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@manishabarse

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I noticed some plots failed because the color mappings did not include pairwise spatial domain (SpD) comparisons (e.g., L1-L2) or the overall ANOVA result. ANOVA gene set enrichment also encountered issues with result column names and single-column data frames being simplified to vectors.

Changes

  • Add color handling for pairwise SpD comparisons by deriving colors from the corresponding domain colors.
  • Use neutral grey for overall ANOVA results, which do not represnt individual SpDs.
  • Standardize ANOVA result column names for downstream plotting.
  • Preserve data frame structure for single-column ANOVA results using drop = FALSE.
  • Add golem:: to app launch function.
  • Add scales to DESCRIPTION file used for color interpolation.

Implementation

  • Automatically generate midpoint colors for pairwise comparisons from the user-supplied colors of the corresponding SpDs, so users do not need to define colors for every pairwise comparison.
  • Use a grey fallback when the colors for the corresponding SpDs are unavailable.
  • Handle overall ANOVA result colors separately from the colors used for enrichment and pairwise statistics.
  • Normalize ANOVA result column names in the app without modifying the original modeling results.

Validation / Testing

  • Tested the updated plotting code locally in RStudio udimg the example from run_app.R script.
  • Also tested the working with current DLPFC_ASD data
  • Verified that ANOVA gene set enrichment and the spatial registration plots SpD color handling work as expected.
  • Checked the plots with @Nick-Eagles and we think ANOVA plots look as would be expected.

…ion heatmap domain colors

- Preserve single-column ANOVA results with drop = FALSE
- Standardize ANOVA result column names
- Add code to handle colors for pairwise comparisons and ANOVA results.

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