StarmapVis: An interactive and narrative visualisation tool for single-cell and spatial data

Ma, Shichao and Fang, Xiunan and Yao, Yu and Li, Jianfu and Morgan, Daniel C. and Xia, Yongyan and Kwok, Crystal S.M. and Lo, Michelle C.K. and Siu, Dickson M.D. and Tsia, Kevin K. and Yang, Andrian and Ho, Joshua W.K. (2023) StarmapVis: An interactive and narrative visualisation tool for single-cell and spatial data. Computational and Structural Biotechnology Journal, 21. pp.1598-1605. ISSN 20010370

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Link to published document: http://doi.org/10.1016/j.csbj.2023.02.023

Abstract

Current single-cell visualisation techniques project high dimensional data into 'map' views to identify high-level structures such as cell clusters and trajectories. New tools are needed to allow the transversal through the high dimensionality of single-cell data to explore the single-cell local neighbourhood. StarmapVis is a convenient web application displaying an interactive downstream analysis of single-cell expression or spatial transcriptomic data. The concise user interface is powered by modern web browsers to explore the variety of viewing angles unavailable to 2D media. Interactive scatter plots display clustering information, while the trajectory and cross-comparison among different coordinates are displayed in connectivity networks. Automated animation of camera view is a unique feature of our tool. StarmapVis also offers a useful animated transition between two-dimensional spatial omic data to three-dimensional single cell coordinates. The usability of StarmapVis is demonstrated by four data sets, showcasing its practical usability. StarmapVis is available at: https://holab-hku.github.io/starmapVis.

Item Type: Article
Subjects: R Medicine > R Medicine (General)
Depositing User: Repository Administrator
Date Deposited: 28 Apr 2023 00:21
Last Modified: 12 Mar 2024 05:14
URI: http://eprints.victorchang.edu.au/id/eprint/1385

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