SpatialCPie：用于空间转录组学聚类评估的 R/Bioconductor 包。
SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation.
机构信息
Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
Department of Bioengineering, Stanford University, California, USA.
出版信息
BMC Bioinformatics. 2020 Apr 29;21(1):161. doi: 10.1186/s12859-020-3489-7.
BACKGROUND
Technological developments in the emerging field of spatial transcriptomics have opened up an unexplored landscape where transcript information is put in a spatial context. Clustering commonly constitutes a central component in analyzing this type of data. However, deciding on the number of clusters to use and interpreting their relationships can be difficult.
RESULTS
We introduce SpatialCPie, an R package designed to facilitate cluster evaluation for spatial transcriptomics data. SpatialCPie clusters the data at multiple resolutions. The results are visualized with pie charts that indicate the similarity between spatial regions and clusters and a cluster graph that shows the relationships between clusters at different resolutions. We demonstrate SpatialCPie on several publicly available datasets.
CONCLUSIONS
SpatialCPie provides intuitive visualizations of cluster relationships when dealing with Spatial Transcriptomics data.
背景
新兴的空间转录组学领域的技术发展开辟了一个未被探索的领域，在这个领域中，转录信息被置于空间背景下。聚类通常是分析这类数据的核心组成部分。然而，决定使用的聚类数量并解释它们之间的关系可能具有挑战性。
结果
我们引入了 SpatialCPie，这是一个专为空间转录组学数据设计的 R 包，用于促进聚类评估。SpatialCPie 可以在多个分辨率下对数据进行聚类。结果以饼图的形式可视化，饼图表示空间区域和聚类之间的相似性，以及聚类图显示不同分辨率下聚类之间的关系。我们在几个公开可用的数据集上演示了 SpatialCPie。
结论
在处理空间转录组学数据时，SpatialCPie 提供了聚类关系的直观可视化。
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