2023年1月20日 · What is a UMAP plot and how to interpret it in single-cell data analysis. Learn the significance of UMAP in visualizing and understanding datasets.

UMAP (Uniform Manifold Approximation and Projection) 算法是一种创新的降维流形学习算法。 来自于拓扑数据分析。 可以用于类似于 t-SNE 的可视化，但也可以用于一般的非线性降维。 文章里的这个图可以看出， sars-cov-2 感染患者的血清 组学数据 与健康个体的组学数据得到了很好的分辨，而其他组则表现出一定程度的分离。 注：示例数据仅作展示用，无实际意义！ 很显然，重点在于umap分析，可视化只是常见的散点图。 #n_neighbors 用似的局部邻域的大小(根据邻域 …

除了之前说过的三种常见单细胞基因可视化方法外，还有一种最常用的就是直接在 UMAP 或者 TSNE 降维图上显示表达某基因的细胞，这种方式更加直观，但是只能显示一个基因，一般用于标记重要的基因。 1、降维可视化. 降维可视化一般用 Dimplot 函数，如果使用的是UMAP方法，可以直接使用UMAPPlot函数，但是感觉效果不好或者很混乱，可以考虑使用 PCAPlot 函数。 可以看到，聚类效果不错，PCA不同细胞群还是分开了。 2、配色及修饰. Seurat 包的函数作图都有默 …

UMAP, at its core, works very similarly to t-SNE - both use graph layout algorithms to arrange data in low-dimensional space. In the simplest sense, UMAP constructs a high dimensional graph representation of the data then optimizes a low-dimensional graph …

2018年12月3日 · Recently, a nonlinear dimensionality-reduction technique, uniform manifold approximation and projection (UMAP), was developed for the analysis of any type of high-dimensional data. Here we apply it to biological data, using three well-characterized mass cytometry and single-cell RNA sequencing datasets.

~4 million single-cell transcriptomes from adult mouse brain labeled by source brain region represented by a UMAP (Yao Z. et al. 2023, bioRxiv). What is a UMAP? This is a special type of graph, called a Uniform Manifold Approximation and Projection (UMAP). UMAPs are helpful ways of displaying many types of data and are often referred to as one ...

2022年10月21日 · In this work, we present the application of UMAP to the analysis of various IFC datasets (including pollen, red blood cells, and monocyte cell line (THP1), demonstrating its ability to facilitate visualization, classification, and tagging of objects from large-scale experiments on complex populations, while working directly on pixel-based image ...

2021年5月3日 · Emerging single-cell technologies profile multiple types of molecules within individual cells. A fundamental step in the analysis of the produced high-dimensional data is their visualization using dimensionality reduction techniques such as t-SNE and UMAP. We introduce j-SNE and j-UMAP as their natu …

2021年4月12日 · UMAP (Uniform Manifold Approximation and Projection) 算法是一种创新的降维流形学习算法。 来自于拓扑数据分析。 可以用于类似于 t-SNE 的可视化，但也可以用于一般的非线性降维。 文章里的这个图可以看出， sars-cov-2 感染患者的血清组学数据与健康个体的组学数据得到了很好的分辨，而其他组则表现出一定程度的分离。 注：示例数据仅作展示用，无实际意义！ 很显然，重点在于umap分析，可视化只是常见的散点图。 umap <- …

2024年9月27日 · Employing Mugen-UMAP, we analyzed whole-exome sequencing data from 365 single-cell samples across 12 non-small cell lung cancer (NSCLC) patients, revealing distinct clusters associated with histological subtypes of NSCLC.