Package: rliger 2.0.1

Yichen Wang

rliger: Linked Inference of Genomic Experimental Relationships

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Authors:Joshua Welch [aut], Yichen Wang [aut, cre], Chao Gao [aut], Jialin Liu [aut], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb], Andrew Robbins [ctb]

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rliger/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/welch-lab/liger/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • bmmc - Liger object of bone marrow subsample data with RNA and ATAC modality
  • pbmc - Liger object of PBMC subsample data with Control and Stimulated datasets
  • pbmcPlot - Liger object of PBMC subsample data with plotting information available

On CRAN:

nonnegative-matrix-factorizationsingle-cell

157 exports 371 stars 6.75 score 78 dependencies 1 dependents 1.0k downloads

Last updated 3 months agofrom:58e5957238

Exports:%<>%%>%as.ligeras.ligerDatasetcalcAgreementcalcAlignmentcalcARIcalcDatasetSpecificitycalcPuritycellMetacellMeta<-closeAllH5commandDiffcommandsconvertOldLigercoordinatecoordinate<-createH5LigerDatasetcreateLigercreateLigerDatasetdatasetdataset<-datasetsdatasets<-defaultClusterdefaultCluster<-defaultDimReddefaultDimRed<-dimReddimRed<-dimRedsdimReds<-downsampleexportInteractTrackfeatureMetafeatureMeta<-getFactorMarkersgetH5FilegetMatrixgetProportionMitoh5fileInfoh5fileInfo<-importBMMCimportCGEimportPBMCimputeKNNis.newLigerisH5LigerligerATACDatasetligerCommandligerMethDatasetligerRNADatasetligerSpatialDatasetligerToSeuratlinkGenesAndPeakslouvainClustermakeFeatureMatrixmakeInteractTrackmakeRiverplotmapCellMetamergeDenseAllmergeH5mergeSparseAllmodalOfnormalizenormalizePeaknormDatanormData<-normPeaknormPeak<-online_iNMFoptimizeALSoptimizeNewDataoptimizeNewKoptimizeNewLambdaoptimizeSubsetplotByDatasetAndClusterplotCellViolinplotClusterDimRedplotClusterFactorDotplotClusterGeneDotplotClusterProportionsplotDatasetDimRedplotDensityDimRedplotDimRedplotEnhancedVolcanoplotFactorDimRedplotFactorHeatmapplotGeneDetectedViolinplotGeneDimRedplotGeneHeatmapplotGeneLoadingRankplotGeneLoadingsplotGeneViolinplotGroupClusterDimRedplotMarkerHeatmapplotPeakDimRedplotProportionplotProportionBarplotProportionDotplotProportionPieplotSankeyplotSpatial2DplotTotalCountViolinplotVarFeaturesplotVolcanoquantile_normquantileAlignSNFquantileNormrawDatarawData<-rawPeakrawPeak<-read10Xread10XATACread10XRNAreadLigerreadSubsetremoveMissingremoveMissingObsrestoreH5LigerrestoreOnlineLigerretrieveCellFeaturereverseMethDatarunCINMFrunClusterrunDoubletFinderrunGeneralQCrunGOEnrichrunGSEArunINMFrunIntegrationrunMarkerDEGrunOnlineINMFrunPairwiseDEGrunTSNErunUINMFrunUMAPrunWilcoxonscaleDatascaleData<-scaleNotCenterscaleUnsharedDatascaleUnsharedData<-selectGenesselectGenesVSTseuratToLigershowsubsetH5LigerDatasetsubsetLigersubsetLigerDatasetsubsetMemLigerDatasetvarFeaturesvarFeatures<-varUnsharedFeaturesvarUnsharedFeatures<-writeH5

Dependencies:BHBiocGenericsbitbit64circlizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayondigestdoParalleldplyrdqrngfansifarverFNNforeachgenericsGetoptLongggplot2ggrepelGlobalOptionsgluegridExtragtablehdf5rigraphIRangesirlbaisobanditeratorslabelinglatticeleidenAlglifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepbmcapplypillarpkgconfigplyrpngpROCR6RANNRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressrjsonrlangRSpectraRtsneS4Vectorsscalessccoreshapesitmotibbletidyselectutf8uwotvctrsviridisviridisLitewithr

Data Integration with LIGER

Rendered fromliger-vignette.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2024-03-27
Started: 2018-10-06

Readme and manuals

Help Manual

Help pageTopics
Generate dot plot from input matrix with ComplexHeatmap.complexHeatmapDotPlot
Produce single violin plot with data frame passed from upstream.ggCellViolin
Generic ggplot theme setting for rliger package.ggplotLigerTheme
Produce single scatter plot with data frame passed from upstream.ggScatter
General heatmap plotting with prepared matrix and data.frames.plotHeatmap
Converting other classes of data to a liger objectas.liger as.liger.dgCMatrix as.liger.Seurat as.liger.SingleCellExperiment seuratToLiger
Converting other classes of data to a ligerDataset objectas.ligerDataset as.ligerDataset.default as.ligerDataset.ligerDataset as.ligerDataset.matrix as.ligerDataset.Seurat as.ligerDataset.SingleCellExperiment
liger object of bone marrow subsample data with RNA and ATAC modalitybmmc
Calculate agreement metric after integrationcalcAgreement
Calculate alignment metric after integrationcalcAlignment
Calculate adjusted Rand index (ARI) by comparing two cluster labeling variablescalcARI
Calculate a dataset-specificity score for each factorcalcDatasetSpecificity
Calculate purity by comparing two cluster labeling variablescalcPurity
Close all links (to HDF5 files) of a liger objectcloseAllH5 closeAllH5.liger closeAllH5.ligerDataset
Check difference of two liger commandcommandDiff
Convert old liger object to latest versionconvertOldLiger
Access ligerSpatialDataset coordinate datacoordinate coordinate,liger,character-method coordinate,ligerSpatialDataset,missing-method coordinate<- coordinate<-,liger,character-method coordinate<-,ligerSpatialDataset,missing-method
Create on-disk ligerDataset ObjectcreateH5LigerDataset
Create liger objectcreateLiger
Create in-memory ligerDataset objectcreateLigerDataset
Downsample datasetsdownsample
Export predicted gene-pair interactionexportInteractTrack
Find shared and dataset-specific markersgetFactorMarkers
Calculate proportion mitochondrial contributiongetProportionMito
Apply function to chunks of H5 data in ligerDataset objectH5Apply
Import prepared dataset publically availableimportBMMC importCGE importPBMC
Impute the peak counts from gene expression data referring to an ATAC dataset after integrationimputeKNN
Check if given liger object if under new implementationis.newLiger
Check if a liger or ligerDataset object is made of HDF5 fileisH5Liger
liger class$.liger $<-.liger c.liger cellMeta cellMeta,liger,character-method cellMeta,liger,missing-method cellMeta,liger,NULL-method cellMeta<- cellMeta<-,liger,character-method cellMeta<-,liger,missing-method commands commands,liger-method dataset dataset,liger,character_OR_NULL-method dataset,liger,missing-method dataset,liger,numeric-method dataset<- dataset<-,liger,character,ANY,ANY,matrixLike-method dataset<-,liger,character,missing,ANY,ligerDataset-method dataset<-,liger,character,missing,ANY,NULL-method datasets datasets,liger-method datasets<- datasets<-,liger,logical-method datasets<-,liger,missing-method defaultCluster defaultCluster,liger-method defaultCluster<- defaultCluster<-,liger,ANY,ANY,character-method defaultCluster<-,liger,ANY,ANY,factor-method defaultCluster<-,liger,ANY,ANY,NULL-method defaultDimRed defaultDimRed,liger-method defaultDimRed<- defaultDimRed<-,liger,character-method dim,liger-method dimnames,liger-method dimnames<-,liger,list-method dimRed dimRed,liger,index-method dimRed,liger,missing_OR_NULL-method dimRed<- dimRed<-,liger,character,ANY,ANY,matrixLike-method dimRed<-,liger,index,ANY,ANY,NULL-method dimReds dimReds,liger-method dimReds<- dimReds<-,liger,list-method fortify.liger getH5File,liger,ANY-method getMatrix,liger,ANY,ANY,ANY-method length.liger lengths.liger liger liger-class names.liger names<-.liger normData,liger-method normData<-,liger,ANY,ANY,H5D-method normData<-,liger,ANY,ANY,matrixLike_OR_NULL-method rawData,liger-method rawData<-,liger,ANY,ANY,H5D-method rawData<-,liger,ANY,ANY,matrixLike_OR_NULL-method scaleData,liger,ANY-method scaleData<-,liger,ANY,ANY,H5D-method scaleData<-,liger,ANY,ANY,H5Group-method scaleData<-,liger,ANY,ANY,matrixLike_OR_NULL-method scaleUnsharedData,liger,character-method scaleUnsharedData,liger,numeric-method scaleUnsharedData<-,liger,ANY,ANY,H5D-method scaleUnsharedData<-,liger,ANY,ANY,H5Group-method scaleUnsharedData<-,liger,ANY,ANY,matrixLike_OR_NULL-method show,liger-method varFeatures varFeatures,liger-method varFeatures<- varFeatures<-,liger,ANY,character-method varUnsharedFeatures varUnsharedFeatures,liger,ANY-method varUnsharedFeatures,ligerDataset,missing-method varUnsharedFeatures<- varUnsharedFeatures<-,liger,ANY,ANY,character-method varUnsharedFeatures<-,ligerDataset,missing,ANY,character-method [[<-.liger
Subclass of ligerDataset for ATAC modalityligerATACDataset ligerATACDataset-class
ligerCommand object: Record the input and time of a LIGER function callligerCommand ligerCommand-class show,ligerCommand-method
ligerDataset classcbind.ligerDataset dim,ligerDataset-method dimnames,ligerDataset-method dimnames<-,ligerDataset,list-method featureMeta featureMeta,ligerDataset-method featureMeta<- featureMeta<-,ligerDataset-method getH5File getH5File,ligerDataset,missing-method getMatrix getMatrix,ligerDataset,ANY,missing,missing-method h5fileInfo h5fileInfo,ligerDataset-method h5fileInfo<- h5fileInfo<-,ligerDataset-method ligerDataset ligerDataset-class normData normData,ligerDataset-method normData<- normData<-,ligerDataset,ANY,ANY,H5D-method normData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method rawData rawData,ligerDataset-method rawData<- rawData<-,ligerDataset,ANY,ANY,H5D-method rawData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method scaleData scaleData,ligerDataset,missing-method scaleData<- scaleData<-,ligerDataset,ANY,ANY,H5D-method scaleData<-,ligerDataset,ANY,ANY,H5Group-method scaleData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method scaleUnsharedData scaleUnsharedData,ligerDataset,missing-method scaleUnsharedData<- scaleUnsharedData<-,ligerDataset,missing,ANY,H5D-method scaleUnsharedData<-,ligerDataset,missing,ANY,H5Group-method scaleUnsharedData<-,ligerDataset,missing,ANY,matrixLike_OR_NULL-method show,ligerDataset-method
Subclass of ligerDataset for Methylation modalityligerMethDataset ligerMethDataset-class
Subclass of ligerDataset for RNA modalityligerRNADataset ligerRNADataset-class
Subclass of ligerDataset for Spatial modalityligerSpatialDataset ligerSpatialDataset-class
Convert between liger and Seurat objectligerToSeurat
Linking genes to putative regulatory elementslinkGenesAndPeaks
[Deprecated] Louvain algorithm for community detectionlouvainCluster-deprecated
Fast calculation of feature count matrixmakeFeatureMatrix
[Deprecated] Export predicted gene-pair interactionmakeInteractTrack-deprecated
[Deprecated] Generate a river (Sankey) plotmakeRiverplot-deprecated
Create new variable from categories in cellMetamapCellMeta
Merge hdf5 filesmergeH5
Merge matrices while keeping the union of rowsmergeDenseAll mergeSparseAll
Return preset modality of a ligerDataset object or that of all datasets in a liger objectmodalOf
Normalize raw counts datanormalize normalize.dgCMatrix normalize.liger normalize.ligerDataset normalize.Seurat normalizePeak
[Deprecated] Perform online iNMF on scaled datasetsonline_iNMF-deprecated
[Deprecated] Perform iNMF on scaled datasetsoptimizeALS-deprecated
Perform factorization for new dataoptimizeNewData
Perform factorization for new value of koptimizeNewK
Perform factorization for new lambda valueoptimizeNewLambda
Perform factorization for subset of dataoptimizeSubset
liger object of PBMC subsample data with Control and Stimulated datasetspbmc
liger object of PBMC subsample data with plotting information availablepbmcPlot
Generate violin/box plot(s) using liger objectplotCellViolin
Make dot plot of factor loading in cell groupsplotClusterFactorDot
Make dot plot of gene expression in cell groupsplotClusterGeneDot
Create density plot basing on specified coordinatesplotDensityDimRed
Generate scatter plot(s) using liger objectplotByDatasetAndCluster plotClusterDimRed plotDatasetDimRed plotDimRed plotFactorDimRed plotGeneDimRed plotPeakDimRed
Plot Heatmap of Gene Expression or Factor LoadingplotFactorHeatmap plotGeneHeatmap
Visualize factor expression and gene loadingplotGeneLoadingRank plotGeneLoadings
Visualize gene expression or cell metadata with violin plotplotGeneDetectedViolin plotGeneViolin plotTotalCountViolin
Comprehensive group splited cluster plot on dimension reduction with proportionplotGroupClusterDimRed
Create heatmap for showing top marker expression in conditionsplotMarkerHeatmap
Visualize proportion across two categorical variablesplotClusterProportions plotProportion plotProportionBar plotProportionDot plotProportionPie
Make Riverplot/Sankey diagram that shows label mapping across datasetsplotSankey
Visualize a spatial datasetplotSpatial2D plotSpatial2D.liger plotSpatial2D.ligerSpatialDataset
Plot the variance vs mean of feature expressionplotVarFeatures
Create volcano plot for Wilcoxon test resultplotEnhancedVolcano plotVolcano
[Deprecated] Quantile align (normalize) factor loadingquantile_norm-deprecated
Quantile align (normalize) factor loadingsquantileAlignSNF
Quantile Align (Normalize) Factor LoadingsquantileNorm quantileNorm.liger quantileNorm.Seurat
Access ligerATACDataset peak datanormPeak normPeak,liger,character-method normPeak,ligerATACDataset,missing-method normPeak<- normPeak<-,liger,character-method normPeak<-,ligerATACDataset,missing-method rawPeak rawPeak,liger,character-method rawPeak,ligerATACDataset,missing-method rawPeak<- rawPeak<-,liger,character-method rawPeak<-,ligerATACDataset,missing-method
Load in data from 10Xread10X read10XATAC read10XRNA
Read liger object from RDS filereadLiger
[Deprecated] See 'downsample'readSubset
Remove missing cells or features from liger objectremoveMissing removeMissingObs
Restore links (to HDF5 files) for reloaded liger/ligerDataset objectrestoreH5Liger restoreOnlineLiger
Retrieve a single matrix of cells from a slotretrieveCellFeature
Create "scaled data" for DNA methylation datasetsreverseMethData
Perform consensus iNMF on scaled datasetsrunCINMF runCINMF.liger runCINMF.Seurat
SNN Graph Based Community DetectionrunCluster
Doublet detection with DoubletFinderrunDoubletFinder
General QC for liger objectrunGeneralQC
Run Gene Ontology enrichment analysis on differentially expressed genes.runGOEnrich
Analyze biological interpretations of metagenerunGSEA
Perform iNMF on scaled datasetsrunINMF runINMF.liger runINMF.Seurat
Integrate scaled datasets with iNMF or variant methodsrunIntegration runIntegration.liger runIntegration.Seurat
Perform online iNMF on scaled datasetsrunOnlineINMF runOnlineINMF.liger runOnlineINMF.Seurat
Find DEG between two groupsrunMarkerDEG runPairwiseDEG runWilcoxon
Perform t-SNE dimensionality reductionrunTSNE
Perform Mosaic iNMF (UINMF) on scaled datasets with unshared featuresrunUINMF runUINMF.liger
Perform UMAP Dimensionality ReductionrunUMAP
Scale genes by root-mean-square across cellsscaleNotCenter scaleNotCenter.dgCMatrix scaleNotCenter.liger scaleNotCenter.ligerDataset scaleNotCenter.ligerMethDataset scaleNotCenter.Seurat
Select a subset of informative genesselectGenes selectGenes.liger selectGenes.Seurat
Select variable genes from one dataset with Seurat VST methodselectGenesVST
Subset liger with bracketssub-liger [.liger
Subset ligerDataset objectsub-ligerDataset [.ligerDataset
Get cell metadata variablesub-sub-liger [[.liger
Subset liger objectsubsetLiger
Subset ligerDataset objectsubsetH5LigerDataset subsetLigerDataset subsetMemLigerDataset
Write in-memory data into H5 filewriteH5 writeH5.default writeH5.dgCMatrix writeH5.liger writeH5.ligerDataset