Package: poem 1.5.0

Siyuan Luo

poem: POpulation-based Evaluation Metrics

This package provides a comprehensive set of external and internal evaluation metrics. It includes metrics for assessing partitions or fuzzy partitions derived from clustering results, as well as for evaluating subpopulation identification results within embeddings or graph representations. Additionally, it provides metrics for comparing spatial domain detection results against ground truth labels, and tools for visualizing spatial errors.

Authors:Siyuan Luo [cre, aut], Pierre-Luc Germain [aut, ctb]

poem_1.5.0.tar.gz
poem_1.5.0.zip(r-4.7)poem_1.5.0.zip(r-4.6)poem_1.5.0.zip(r-4.5)
poem_1.5.0.tgz(r-4.6-any)poem_1.5.0.tgz(r-4.5-any)
poem_1.5.0.tar.gz(r-4.7-any)poem_1.5.0.tar.gz(r-4.6-any)
poem_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
poem/json (API)

# Install 'poem' in R:
install.packages('poem', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/roseyuan/poem/issues

Pkgdown/docs site:https://roseyuan.github.io

Datasets:

On BioConductor:poem-1.5.0(bioc 3.24)poem-1.4.0(bioc 3.23)

dimensionreductionclusteringgraphandnetworkspatialatacseqsinglecellrnaseqsoftwarevisualization

6.52 score 11 stars 25 scripts 242 downloads 24 exports 99 dependencies

Last updated from:cc13550956. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE261
linux-devel-x86_64OK545
source / vignettesOK584
linux-release-x86_64OK522
macos-release-arm64OK259
macos-oldrel-arm64OK335
windows-develOK914
windows-releaseOK519
windows-oldrelOK910
wasm-releaseOK210

Exports:CDbwCHAOSdbcvELSAemb2knnemb2snnfindSpatialKNNfuzzyHardMetricsfuzzyHardSpotConcordancefuzzyPartitionMetricsgetEmbeddingMetricsgetFuzzyLabelgetFuzzyPartitionMetricsgetGraphMetricsgetNeighboringPairConcordancegetPartitionMetricsgetSpatialExternalMetricsgetSpatialInternalMetricsknnCompositionmatchSetsmockDataPASsilhouetteWidthsspatialARI

Dependencies:abindaricodeaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelbitbit64blobblusterbootcachemclassclassIntclevrcliclueclustercodetoolscpp11curlDBIdbplyrDelayedArraydeldirdplyre1071elsafastmapfclustfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2igraphIRangesKernSmoothlambda.rlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustcompmemoiseopensslpdistpillarpkgconfigproxypurrrR6rappdirsrasterrbibutilsRcppRcppArmadilloRdpackrjsonrlangRSQLites2S4ArraysS4VectorsSeqinfosfSingleCellExperimentsnowspSparseArraySpatialExperimentspDataspdepstringistringrSummarizedExperimentsysterratibbletidyrtidyselectunitsutf8vctrswithrwkXVector

Details about each evaluation metrics
Introduction | Partition-based metrics | Embedding-based metrics | Graph-based metrics | Metrics for spatial clusterings | Session info
Rendered fromMetricsInPoem.rmdusingknitr::rmarkdown

Last update: 2025-06-03
Started: 2025-04-10

Introduction to poem
Installation & loading | Introduction | What is this package for? | Main functions | Getting started | Example data | Embedding evaluation | Element-level evaluation | Class-level evaluation | Dataset-level evaluation | Graph evaluation | Partition evaluation | Fuzzy partition evaluation | Spatial clustering evaluation | External metrics | Internal metrics | Session info
Rendered frompoem.Rmdusingknitr::rmarkdown

Last update: 2025-04-14
Started: 2024-10-19

Working with SpatialExperiment
Prepare dataset | Calculate external spatial metrics | Dataset level | Class/cluster level | Element level | Calculate internal spatial metrics | Session info
Rendered fromPoemOnSpatialExperiment.Rmdusingknitr::rmarkdown

Last update: 2025-04-14
Started: 2025-04-10

Readme and manuals

Help Manual

Help pageTopics
Calculate CDbw indexCDbw
Calculate CHAOS scoreCHAOS
Calculate DBCV Metricdbcv
Calculate ELSA scoresELSA
Computes k nearest neighbors from embeddingemb2knn
Computes shared nearest neighbors from embeddingemb2snn
Find the k nearest spatial neighborsfindSpatialKNN
Compute fuzzy-hard versions of pair-sorting partition metricsfuzzyHardMetrics
Per-element maximal concordance between a hard and a fuzzy partitionfuzzyHardSpotConcordance
Compute fuzzy-fuzzy versions of pair-sorting partition metricsfuzzyPartitionMetrics
Compute embedding-based metricsgetEmbeddingMetrics
Get fuzzy representation of labelsgetFuzzyLabel
Compute external metrics for fuzzy clusteringsgetFuzzyPartitionMetrics
Compute graph-based metricsgetGraphMetrics
Per-element local concordance between a clustering and a ground truthgetNeighboringPairConcordance
Per-element pair concordance scoregetPairConcordance
Compute partition-based metricsgetPartitionMetrics
Calculate Spatial External MetricsgetSpatialExternalMetrics getSpatialExternalMetrics,missing-method getSpatialExternalMetrics,SpatialExperiment-method
Compute internal metrics for spatial datagetSpatialInternalMetrics getSpatialInternalMetrics,missing-method getSpatialInternalMetrics,SpatialExperiment-method
Compute neighborhood compositionknnComposition
Match two partitions using Hungarian algorithmmatchSets
Metrics Informationmetric_info
Generate mock multidimensional datamockData
The noisy moon datasetnoisy_moon
Calculate PAS scorePAS
Toy examples of spatial datasp_toys
Spatially aware ARI from Yan, Yinqiao, et al. (2025).spatialARI
Toy embedding examplestoyExamples