Making HTML Slides with the litedown Package

Mon, 01 Jan 0001 00:00:00 +0000

Introduction

cw

2026-03-02

1 项目成果展示：胃癌多组学研究设计
2 项目成果展示：生信可视化
3 项目成果展示：单细胞分析可视化
4 easybio

1 项目成果展示：胃癌多组学研究设计

graph TB;

 subgraph Phase I: Data Collection & Pre-processing
 direction TB;
 Data_SC["<b>scRNA-seq Datasets</b><br/>(GSE datasets)<br/><i>Identification of cell types</i>"];
 Data_Bulk["<b>Bulk Transcriptome</b><br/>Training: TCGA-gastric cancer<br/>Validation: GEO Cohorts"];
 Data_Multi["<b>Multi-omics Data</b><br/>Mutation, CNV, Methylation<br/>HPA (IHC), Drug Databases"];
 end

 subgraph Phase II: Identification of FRGs
 direction TB;
 Step_Clustering["Seurat Clustering & SingleR Annotation<br/>(Immune, Stromal, Malignant cells)"];
 Step_Screening["Screening Fibroblast-Related Genes (FRGs)<br/>High expression in fibroblast clusters"];
 Step_Validation["Cross-Validation<br/>(TISCH DB & Correlation with<br/>xCell/MCP-counter)"];
 Node_54FRGs{"<b>Candidate FRGs</b><br/>Identified"};
 end
 
 subgraph Phase III: FRGI Model Construction
 direction TB;
 Step_Omics["Multi-omics Characterization<br/>(Diff. Exp, Mutation, CNV, Methylation)"];
 Step_Drug["Clinical Value Assessment<br/>(PubTator, TDL, Gene Dependency Score)"];
 Step_ML["<b>Machine Learning Selection</b><br/>10 Algorithms Integration<br/>(Lasso, Ridge, RF, GBM, Boruta, etc.)"];
 Node_3Genes{"<b>Core Signature (FRGI)</b>"};
 end

 subgraph Phase IV: CD8+ T-cell - Fibroblast Subtyping
 direction TB;
 Step_Class1["<b>FRG Subtyping</b><br/>Fibroblast Hot vs. Cold"];
 Step_Mechanism["Mechanism Analysis<br/>GSEA, GSVA, TIDE (Immunotherapy)"];
 Step_Class2["<b>Dual-Factor Subtyping<br/>Construction</b><br/>CD8+ T-cell Activity <b>x</b> FRG Status"];
 Outcome_4Types["<b>Four Molecular Subtypes</b><br/>CD8+FH, CD8+FC, CD8-FH, CD8-FC"];
 end

 Step_Nomogram["Nomogram Construction<br/>FRGI + Clinical Variables"];
 Step_SurvVal["Survival Validation<br/>(TCGA, GEO, Pan-cancer)"];
 Outcome_Therapy["<b>Therapeutic Strategy Map</b><br/>Precision Medicine Guidance<br/>(Immuno/Chemo/Targeted Therapy)"];

 Data_SC --> Step_Clustering;
 Step_Clustering --> Step_Screening;
 Step_Screening --> Step_Validation;
 Step_Validation --> Node_54FRGs;
 
 Node_54FRGs --> Step_Omics;
 Node_54FRGs --> Step_Drug;

 Data_Multi --> Step_Omics;
 
 Step_Omics --> Step_ML;
 Step_Drug --> Step_ML;
 Data_Bulk -- "Expression Data" --> Step_ML;
 
 Step_ML --> Node_3Genes;
 Node_3Genes --> Step_Nomogram;
 Node_3Genes --> Step_SurvVal;
 
 Node_3Genes --> Step_Class1;
 Step_Class1 --> Step_Mechanism;
 Step_Mechanism -- "Integrate with<br/>CD8+ T-cell Signature" --> Step_Class2;
 Step_Class2 --> Outcome_4Types;
 
 Outcome_4Types --> Outcome_Therapy;
 Step_Nomogram -. "Clinical Prediction" .-> Outcome_Therapy;
 Step_SurvVal --> Outcome_Therapy;

 %% Styling
 style Data_SC fill:#E3F2FD,stroke:#1565C0,stroke-width:1.5px;
 style Data_Bulk fill:#E3F2FD,stroke:#1565C0,stroke-width:1.5px;
 style Data_Multi fill:#E3F2FD,stroke:#1565C0,stroke-width:1.5px;

 style Step_Clustering fill:#E0F2F1,stroke:#00695C,stroke-width:1.5px;
 style Step_Screening fill:#E0F2F1,stroke:#00695C,stroke-width:1.5px;
 style Step_Validation fill:#E0F2F1,stroke:#00695C,stroke-width:1.5px;
 style Node_54FRGs fill:#B2DFDB,stroke:#00695C,stroke-width:1.5px;

 style Step_Omics fill:#FFF3E0,stroke:#EF6C00,stroke-width:1.5px;
 style Step_Drug fill:#FFF3E0,stroke:#EF6C00,stroke-width:1.5px;
 style Step_ML fill:#FFF3E0,stroke:#EF6C00,stroke-width:1.5px;
 style Node_3Genes fill:#FFE0B2,stroke:#EF6C00,stroke-width:1.5px;

 style Step_Nomogram fill:#F3E5F5,stroke:#6A1B9A,stroke-width:1.5px;
 style Step_SurvVal fill:#F3E5F5,stroke:#6A1B9A,stroke-width:1.5px;
 
 style Step_Class1 fill:#FFEBEE,stroke:#C62828,stroke-width:1.5px;
 style Step_Mechanism fill:#FFEBEE,stroke:#C62828,stroke-width:1.5px;
 style Step_Class2 fill:#FFEBEE,stroke:#C62828,stroke-width:2.5px;

 style Outcome_4Types fill:#FAFAFA,stroke:#333333,stroke-width:1.5px;
 style Outcome_Therapy fill:#FAFAFA,stroke:#333333,stroke-width:1.5px;

Nightingale

Making HTML Slides with the litedown Package

Yihui Xie

`{r} Sys.Date()`

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Introduction

cw

2026-03-02

1 项目成果展示：胃癌多组学研究设计

2 项目成果展示：生信可视化