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poem: POpulation-based Evaluation Metrics

Overview

The poem package provides multiple metrics for evaluating subpopulation structure identification in a dataset. These include:

  • Metrics for comparing two partitions1 of the same dataset, or metrics evaluating the alignment between a dataset’s embedding or graph representations with its partition.

  • Metrics for comparing two fuzzy partitions2, or for comparing a hard partition with a fuzzy partition. This allows the evaluation of fuzzy partition results by assessing its agreement to a fuzzy or a hard ground-truth partition.

  • Metrics tailored for domain detection in spatially-resolved omics data. These include especially external evaluation metrics (i.e. based on a comparison to ground truth labels), but also internal metrics.

For a detailed introduction of the package, see the online docs.

Installation

poem is available through Bioconductor, and can be installed using the following commands:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("poem")

Contact

In case you have any questions or suggestions to poem, please consider opening an issue to the GitHub repository.