Extract heatmap core logic into testable R package functions

[Copilot]

Heatmap visualization logic was embedded in Shiny module, making it untestable and unreusable. Extracted into proper package functions with comprehensive test coverage.

Changes

New package functions (R/vis_custom_heatmap.R):

• parse_custom_groups() - Parse group definition strings
• prepare_heatmap_data() - Transform data to long format with grouping
• generate_custom_heatmap() - Core visualization with tidyHeatmap
• vis_custom_heatmap() - High-level wrapper

Test coverage (tests/testthat/test-vis_custom_heatmap.R):

• 21 test cases covering all functions, edge cases, and error handling

Shiny module refactoring:

• Replaced 100 lines of embedded logic with package function calls
• Module now handles only UI reactivity and display

Usage

Functions are now independently usable:

library(UCSCXenaShiny)

data <- data.frame(
  sample = rep(paste0("S", 1:20), each = 10),
  gene = rep(paste0("Gene", 1:10), 20),
  value = rnorm(200)
)

groups <- "Responders: S1,S2,S3,S4,S5\nNon-responders: S6,S7,S8,S9,S10"

hm <- vis_custom_heatmap(
  data = data,
  groups = groups,
  color_palette = "viridis",
  cluster_rows = TRUE
)

Architecture

Before: Monolithic Shiny module (500 lines, untestable)
After: Package functions (356 lines) + thin Shiny wrapper (450 lines)

All core logic is now testable without Shiny, reusable in scripts/pipelines, and properly documented with roxygen2.

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[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

[lishensuo]

@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~

[ShixiangWang]

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]

@copilot 只引入 tidyHeatmap 作为 suggests 依赖实现目标功能，请重新实现和测试。

[Copilot]

@copilot 只引入 tidyHeatmap 作为 suggests 依赖实现目标功能，请重新实现和测试。

Refactoring complete! The custom heatmap module now uses only tidyHeatmap as a Suggests dependency.

Key changes:

• Removed 5 packages (ComplexHeatmap, pheatmap, viridis, circlize, grid)
• Kept only tidyHeatmap
• Reduced code by 196 lines (~28%)
• All features preserved
• Added comprehensive documentation

Commits:

• dcda177 - Main refactoring
• 68f7236 - Code clarity improvements
• d6bbd53 - Address code review feedback
• b9f1315 - Add documentation

Ready for testing. All functionality including custom grouping, multiple color palettes, and export features have been preserved.

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