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verified publisher icon openbiox

Implement custom grouped heatmap feature for expression data visualization

Open Copilot opened this issue 6 months ago • 3 comments

This PR implements a comprehensive custom grouped heatmap feature that addresses the need for "自定义分组热图" (Custom Grouped Heatmap) functionality in UCSCXenaShiny.

Key Features

Custom Sample Grouping

The implementation supports two flexible grouping methods:

  • Manual Definition: Users can define custom sample groups using an intuitive format: 
    Group1: TCGA-AA-3502,TCGA-AA-3506,TCGA-AA-3514
Group2: TCGA-AA-3510,TCGA-AA-3520,TCGA-AA-3524
  • Phenotype-based: Automatic grouping using existing phenotype variables from clinical data

Expression Data Visualization

  • Displays expression data with genes as rows and samples as columns (as requested)
  • Multi-gene selection with search functionality
  • Support for both UCSC Xena datasets and custom uploaded data
  • Configurable gene limits (5-500 genes) for performance optimization

Advanced Visualization Options

  • Multiple clustering methods (complete, average, single, ward.D, etc.)
  • Rich color palette selection (viridis, plasma, RdYlBu, Spectral, etc.)
  • Configurable display options (gene names, sample names, clustering toggles)
  • Visual group annotations displayed as colored bars above the heatmap

Technical Implementation

  • Multi-backend Support: Uses ComplexHeatmap as primary backend with pheatmap fallback for broader compatibility
  • Robust Data Handling: Includes error handling, data validation, and missing value management
  • Export Functionality: Download support for PNG/PDF formats with proper handling for different plot types
  • UI Integration: Seamlessly integrated as new "Custom-Heatmap" tab in General Analysis page

Usage Workflow

  1. Navigate to General Analysis → Custom-Heatmap tab
  2. Select dataset or upload custom data
  3. Choose genes/features for visualization
  4. Configure appearance (clustering, colors, labels)
  5. Define sample groups (custom or phenotype-based)
  6. Generate heatmap with group annotations
  7. Download results in preferred format

Files Changed

  • New Module: inst/shinyapp/modules/01_general/modules-ga-custom-heatmap.R
  • UI Integration: inst/shinyapp/ui/general-analysis.R
  • Server Integration: inst/shinyapp/server/general-analysis.R
  • Dependencies: Added ComplexHeatmap, pheatmap, viridis, circlize, grid to DESCRIPTION

This implementation provides the exact functionality requested for custom grouped heatmap visualization and establishes a solid foundation for future enhancements, such as overlaying different molecular data types.

Fixes #218.

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Copilot avatar Aug 26 '25 03:08 Copilot

@lishensuo 有空看看ai的代码写的怎么样哈？是不是改改就能合并

ShixiangWang avatar Aug 26 '25 04:08 ShixiangWang

@lishensuo 有空看看ai的代码写的怎么样哈？是不是改改就能合并

收到老师。等周末左右的时候，会一起处理下~

lishensuo avatar Aug 26 '25 05:08 lishensuo

嗯，这个就玩一玩看看，有空搞搞就行，不着急 ---- 回复的原邮件 ---- 发件人 @.> 日期 2025年08月26日 13:04 收件人 @.> 抄送至 Shixiang Wang @.>@.> 主题 Re: [openbiox/UCSCXenaShiny] Implement custom grouped heatmap feature for expression data visualization (PR #375) lishensuo left a comment (openbiox/UCSCXenaShiny#375) @lishensuo 有空看看ai的代码写的怎么样哈？是不是改改就能合并 收到老师。等周末左右的时候，会一起处理下~ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were assigned.Message ID: @.***>

ShixiangWang avatar Aug 26 '25 05:08 ShixiangWang