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-any)poem_1.5.0.zip(r-4.6-any)poem_1.5.0.zip(r-4.5-any)
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

4.79 score 11 stars 28 scripts 298 downloads 24 exports 99 dependencies

Last updated from:cc13550956. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE232
linux-develWARNING579
source / vignettesERROR388
linux-releaseWARNING561
macos-releaseWARNING396
macos-oldrelWARNING406
windows-develWARNING551
windows-releaseWARNING407
windows-oldrelWARNING483
wasm-releaseOK201

Exports:CDbwCHAOSdbcvELSAemb2knnemb2snnfindSpatialKNNfuzzyHardMetricsfuzzyHardSpotConcordancefuzzyPartitionMetricsgetEmbeddingMetricsgetFuzzyLabelgetFuzzyPartitionMetricsgetGraphMetricsgetNeighboringPairConcordancegetPartitionMetricsgetSpatialExternalMetricsgetSpatialInternalMetricsknnCompositionmatchSetsmockDataPASsilhouetteWidthsspatialARI

Dependencies:abindaricodeaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelbitbit64blobblusterbootcachemclassclassIntclevrcliclueclustercodetoolscpp11curlDBIdbplyrDelayedArraydeldirdigestdplyre1071elsafastmapfclustfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2igraphIRangesKernSmoothlambda.rlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustcompmemoiseopensslpdistpillarpkgconfigproxypurrrR6rasterrbibutilsRcppRcppArmadilloRdpackrjsonrlangRSQLites2S4ArraysS4VectorsSeqinfosfSingleCellExperimentsnowspSparseArraySpatialExperimentspDataspdepstringistringrSummarizedExperimentsysterratibbletidyrtidyselectunitsutf8vctrswithrwkXVector

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