Peer Review Report For: Interactive visualization of spatial omics neighborhoods [version 1; peer review: 2 approved with reservations]
Year: 2024
Type: peer-review
Abstract: Dimensionality reduction of spatial omic data can reveal shared, spatially structured patterns of expression across a collection of genomic features. We studied strategies for discovering and interactively visualizing low-dimensional structure in spatial omic data based on the construction of neighborhood features. We designed quantile and network-based spatial features that result in spatially consistent embeddings. A simulation compares embeddings made with and without neighborhood-based featurization, and a re-analysis of Keren et al. , 2019 illustrates the overall workflow. We provide an R package, NBFvis, to support computation and interactive visualization for the proposed dimensionality reduction approach. Code and data for reproducing experiments and analysis are available on GitHub .
Authors: Tinghui Xu, Kris Sankaran
Institution: University of Wisconsin–Madison
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4416633828
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