cGAP用三维嵌入可视化高维分类数据,保留原始矩阵并显式呈现模式结构。
cGAP: Generalized Association Plots with HOMALS-Guided Heatmaps for Visualization of High-Dimensional Categorical Data

- 基于HOMALS将类别和样本嵌入三维空间,映射为红绿蓝颜色
- 通过重排序揭示聚类、异常值及局部到全局的结构特征
- 适合需要透明可追溯分析的生物、社会科学研究者
高维分类数据广泛存在于遗传学、生物医学与社会科学中,但其可视化工具远落后于连续变量。现有方法或扩展性差,或依赖脱离原始数据矩阵的低维展示,或牺牲可解释性以追求预测精度。为此,我们提出分类广义关联图(cGAP),一种针对名义、有序与二元数据的可视化框架,保留原始数据矩阵的同时,引入可解释的几何结构。cGAP利用同质性分析(HOMALS)将样本与类别水平嵌入三维欧几里得空间,并将其映射为红-绿-蓝色彩,使相似模式呈现相似颜色。该框架集成三个协同视图:原始数据矩阵的HOMALS引导热图、样本邻近矩阵与变量邻近矩阵。序列算法用于重排行列,以揭示连贯聚类、异常值及局部到全局结构。我们推导出重心可追溯性、投影失真与对比度保持等性质,阐明嵌入几何如何传递至可视化。通过学生-动物分类、哺乳动物齿列、UCI蘑菇数据集及正交基因簇数据库的应用,验证了cGAP在跨科学领域支持透明探索性分析的能力,实现全矩阵、基于热图的复杂分类数据可视化。
原文摘要 · Abstract (English)
High-dimensional categorical data arise in genetics, biomedicine, and the social sciences, yet visualization tools for such data remain far less developed than those for continuous variables. Existing methods either scale poorly, rely heavily on low-dimensional displays detached from the original data matrix, or prioritize predictive accuracy over interpretability. To address this gap, we introduce categorical Generalized Association Plots (cGAP), a visualization framework for nominal, ordinal, and binary data that preserves the original data matrix while augmenting it with interpretable geometric structure. cGAP uses Homogeneity Analysis (HOMALS) to embed subjects and category levels in a three-dimensional Euclidean space and maps the embedding to red-green-blue coordinates so that similar patterns receive similar colors. The framework integrates three coordinated views: a HOMALS-guided heatmap of the raw data matrix, a subject proximity matrix, and a variable proximity matrix. Seriation algorithms are then used to reorder rows and columns to reveal coherent clusters, outliers, and local-to-global structure. We also derive barycentric traceability, projection-distortion, and contrast-preservation properties that clarify how embedding geometry is transferred to the display. We demonstrate the versatility of cGAP through applications to student-animal classification data, mammalian dentition profiles, mushroom records from the UCI Machine Learning Repository, and the Clusters of Orthologous Genes database. These examples show that cGAP supports transparent exploratory analysis by maintaining traceability between derived visual structure and the original categorical observations. cGAP provides a full-matrix, heatmap-based visualization environment for investigating complex categorical datasets across scientific domains.
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