219 lines
6.1 KiB
Markdown
219 lines
6.1 KiB
Markdown
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# 2026-03-28 ~ 2026-03-29 工作记录 - bbav20311 Promoter分析可视化优化
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> 日期: 2026-03-28 15:09 ~ 2026-03-29 02:00
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> 参与: xialab的幸运星
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> 主题: Promoter分析模块可视化升级与热图融合
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---
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## 1. 工作目标
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优化Promoter（启动子顺式作用元件）分析模块的可视化输出，融合多种热图绘制方法，创建更符合发表要求的组合图。
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---
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## 2. 主要工作内容
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### 2.1 热图绘制方法对比与融合
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| 脚本 | 来源 | 特点 | 问题 |
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|:---|:---|:---|:---|
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| `promoter_v4_final.R` | 现有V4版本 | 7大分类、外部树图、红绿配色 | 连续渐变不够清晰 |
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| `promoter_analysis_complete.R` | complete版本 | 方块+数字、蓝白分级 | 元件命名处理逻辑有问题 |
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| `promoter_v5_fused_heatmap.R` | **融合版** | V4分类 + complete显示方式 | ✅ 采用 |
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**融合策略**:
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- 保留V4的7大分类逻辑
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- 采用complete的方块+数字显示
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- 9级蓝白分级配色
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### 2.2 5面板组合图开发 (V6)
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创建全新的5面板组合图布局：
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```
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A (左) B (中左) C (中) D (右) E (最右)
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进化树 + 亚家族竖线 + 7大分类堆叠 + 热图(方块+数字) + 图例
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```
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**文件**: `scripts/promoter_v6_combined.R`
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**特点**:
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- 画布自动调整 (9000×6000)
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- Panel C宽度增加 (8 → 12)
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- 热图方格为正方形
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- 实线边框 (grey60)
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- 0值显示白色背景
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### 2.3 集成到分析流程
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修改 `apps/cli/run_promoter.py`:
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1. **集成V6脚本** - 自动生成5面板组合图
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2. **保留其他统计图** - 甜甜圈、柱形图、UpSet等
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3. **移除旧版** - `_02_combined.png` 不再生成
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4. **修复manifest** - 添加`figures`字段供前端显示
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---
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## 3. 关键修改文件
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### 3.1 新增/修改的R脚本
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| 文件 | 路径 | 说明 |
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| `promoter_v5_fused_heatmap.R` | `scripts/` | 融合版热图 (V5) |
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| `promoter_v6_combined.R` | `scripts/` | **5面板组合图 (V6)** |
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### 3.2 修改的Python脚本
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| 文件 | 路径 | 修改内容 |
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| `run_promoter.py` | `apps/cli/` | 集成V6，添加figures字段 |
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### 3.3 生成的可视化文件
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| 文件 | 说明 |
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| `Ft.SPL_promoter_v6_combined.png` | **新版5面板组合图** |
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| `Ft.SPL_promoter_01_heatmap.png` | 独立热图 |
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| `Ft.SPL_promoter_03_element_barplot.png` | 元件柱形图 |
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| `Ft.SPL_promoter_03b_big7_barplot.png` | 7大分类柱形图 |
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| `Ft.SPL_promoter_04_category_stacked.png` | 分类堆叠图 |
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| `Ft.SPL_promoter_05_upset.png` | UpSet图 |
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| `Ft.SPL_promoter_06_category_donut.png` | 甜甜圈图 |
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---
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## 4. 7大分类定义
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| 分类 | 颜色 | 包含元件 |
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|:---|:---|:---|
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| Core promoter | #e41a1c | TATA-box, CAAT-box, Inr, Y-patch |
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| Light response | #377eb8 | G-box, GT1, I-box, Sp1, Box.4, GATA |
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| Hormone signaling | #4daf4a | ABRE, GARE, CGTCA, TCA, TGA, ERE |
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| Stress response | #984ea3 | DRE, LTR, ARE, STRE, W-box |
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| TF binding | #ff7f00 | MYB, MYC, WRKY |
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| Development | #f781bf | RY, AAGAA, CAT, GCN4 |
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| Other | #999999 | 未分类 |
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---
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## 5. 技术细节
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### 5.1 热图颜色分级
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```r
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count_colors <- c(
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"[0,1)" = "#f7fbff", # 白色（0值）
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"[1,2)" = "#c6dbef", # 浅蓝
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"[2,3)" = "#9ecae1",
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"[3,5)" = "#6baed6",
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"[5,10)" = "#4292c6",
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"[10,20)" = "#2171b5",
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"[20,50)" = "#08519c",
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"[50,100)"= "#08306b",
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"[100,200]"="#041d3a" # 深蓝
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)
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```
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### 5.2 画布自适应计算
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```r
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# 根据内容自动计算画布大小
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total_width <- (x_D_right - x_A_left) + 3 # 加上图例空间
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total_height <- max_y + 2
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max_width <- 30
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max_height <- 20
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final_width <- min(total_width, max_width)
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final_height <- min(total_height, max_height)
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```
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---
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## 6. 测试结果
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### 6.1 测试任务
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- **任务ID**: job_1774711833127
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- **基因**: 24个 Ft.SPL 基因
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- **启动子元件**: 3699条记录
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### 6.2 生成文件验证
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```bash
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$ ls final/Ft.SPL_promoter*.png
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Ft.SPL_promoter_01_heatmap.png (131K)
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Ft.SPL_promoter_03b_big7_barplot.png (38K)
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Ft.SPL_promoter_03_element_barplot.png (21K)
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Ft.SPL_promoter_04_category_stacked.png (68K)
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Ft.SPL_promoter_05_upset.png (32K)
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Ft.SPL_promoter_06_category_donut.png (60K)
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Ft.SPL_promoter_v6_combined.png (701K) # 新版5面板
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```
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### 6.3 Manifest验证
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```json
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{
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"figures": [
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{"name": "Ft.SPL_promoter_01_heatmap", ...},
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{"name": "Ft.SPL_promoter_03_element_barplot", ...},
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{"name": "Ft.SPL_promoter_03b_big7_barplot", ...},
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{"name": "Ft.SPL_promoter_04_category_stacked", ...},
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{"name": "Ft.SPL_promoter_05_upset", ...},
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{"name": "Ft.SPL_promoter_06_category_donut", ...},
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{"name": "Ft.SPL_promoter_v6_combined", ...} # 新版
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]
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}
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```
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---
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## 7. 问题与解决
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| 问题 | 原因 | 解决方案 |
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| V6图不显示在结果中 | manifest缺少figures字段 | 添加figures数组 |
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| 堆叠图太拥挤 | Panel C宽度不足 | width_C从8增加到12 |
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| 热图方格变形 | element_width设置不当 | 改为正方形 (gene_height * 2) |
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| 旧版_02_combined仍在生成 | 未移除V2调用 | 修改流程，只生成V6和其他统计图 |
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| 其他统计图丢失 | V2调用被跳过 | 先运行V6，再运行V2生成其他图 |
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---
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## 8. 时间记录
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| 时间段 | 时长 | 内容 |
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| 15:09 - 17:18 | 2小时 | 分析热图绘制方法，创建V5融合版 |
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| 17:18 - 20:00 | 3小时 | 开发V6 5面板组合图 |
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| 20:00 - 23:30 | 3.5小时 | 集成到流程，修复manifest |
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| 23:30 - 02:00 | 2.5小时 | 调试优化，测试验证 |
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| **总计** | **11小时** | **完成所有目标** |
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---
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## 9. 状态
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- **V5融合版热图**: ✅ 完成
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- **V6 5面板组合图**: ✅ 完成
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- **集成到分析流程**: ✅ 完成
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- **manifest修复**: ✅ 完成
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- **测试验证**: ✅ 通过
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---
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## 10. 下一步建议
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1. **用户反馈收集** - 根据实际使用调整面板宽度
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2. **颜色方案优化** - 如有需要可调整7大分类颜色
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3. **字体大小调整** - 根据期刊要求调整
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4. **批量测试** - 测试更多基因家族数据
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---
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*记录时间: 2026-03-29 02:00*
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*记录位置: `/home/xia-lab/wutx/00test/bbav20311/memory/2026-03-28.md`*
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*状态: ✅ 已保存*
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