Package: rliger 2.2.1.9002

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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rliger/json (API)

# Install 'rliger' in R:

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

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

Pkgdown/docs site:https://welch-lab.github.io

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
ccGeneHuman - Cell cycle gene set for human
deg.marker - Data frame for example marker DEG test result
deg.pw - Data frame for example pairwise DEG test result
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-factorization single-cell openblas cpp

10.62 score 431 stars 2 packages 498 scripts 1.5k downloads 178 exports 75 dependencies

Last updated from:a41973c68d. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	529
linux-devel-x86_64	OK	641
source / vignettes	OK	615
linux-release-arm64	OK	549
linux-release-x86_64	OK	664
macos-release-arm64	OK	369
macos-release-x86_64	OK	621
macos-oldrel-arm64	OK	343
macos-oldrel-x86_64	OK	676
windows-devel	OK	567
windows-release	OK	517
windows-oldrel	OK	548
wasm-release	OK	437

Exports:%<>%%>%alignFactors as.liger as.ligerDataset calcAgreement calcAlignment calcARI calcDatasetSpecificity calcNMI calcPurity cellMeta cellMeta<-centroidAlign closeAllH5 commandDiff commands convertOldLiger coordinate coordinate<-createH5LigerDataset createLiger createLigerDataset dataset dataset<-datasets datasets<-defaultCluster defaultCluster<-defaultDimRed defaultDimRed<-dimRed dimRed<-dimReds dimReds<-downsample element_line_fixlen exportInteractTrack factorGSEA featureMeta featureMeta<-getFactorMarkers getH5File getMatrix getProportionMito h5fileInfo h5fileInfo<-importBMMC importCGE importPBMC imputeKNN is.newLiger isH5Liger ligerATACDataset ligerCommand ligerMethDataset ligerRNADataset ligerSpatialDataset ligerToSeurat linkGenesAndPeaks louvainCluster makeFeatureMatrix makeInteractTrack makeRiverplot mapCellMeta mergeDenseAll mergeH5 mergeSparseAll modalOf normalize normalizePeak normData normData<-normPeak normPeak<-online_iNMF optimizeALS optimizeNewData optimizeNewK optimizeNewLambda optimizeSubset plotBarcodeRank plotByDatasetAndCluster plotCellViolin plotClusterDimRed plotClusterFactorDot plotClusterGeneDot plotClusterGeneViolin plotClusterProportions plotDatasetDimRed plotDensityDimRed plotDimRed plotEnhancedVolcano plotFactorDimRed plotFactorHeatmap plotGeneDetectedViolin plotGeneDimRed plotGeneHeatmap plotGeneLoadingRank plotGeneLoadings plotGeneViolin plotGODot plotGroupClusterDimRed plotMarkerHeatmap plotPairwiseDEGHeatmap plotPeakDimRed plotProportion plotProportionBar plotProportionBox plotProportionDot plotProportionPie plotSankey plotSpatial2D plotTotalCountViolin plotVarFeatures plotVolcano quantile_norm quantileAlignSNF quantileNorm rawData rawData<-rawPeak rawPeak<-read10X read10XATAC read10XFiles read10XH5 read10XH5Delay read10XH5Mem read10XRNA readH5AD readH5ADDelay readH5ADMem readLiger readSubset removeMissing removeMissingObs restoreH5Liger restoreOnlineLiger retrieveCellFeature reverseMethData runCINMF runCluster runGeneralQC runGOEnrich runGSEA runINMF runIntegration runMarkerDEG runOnlineINMF runPairwiseDEG runTSNE runUINMF runUMAP runWilcoxon scaleData scaleData<-scaleNotCenter scaleUnsharedData scaleUnsharedData<-selectBatchHVG selectGenes selectGenesVST seuratToLiger show subsetH5LigerDataset subsetLiger subsetLigerDataset subsetMemLigerDataset suggestK theme_axis_shortArrow updateLigerObject varFeatures varFeatures<-varUnsharedFeatures varUnsharedFeatures<-writeH5 writeH5AD

Dependencies:abind backports BH BiocGenerics biocmake bit bit64 checkmate cli cpp11 DelayedArray dir.expiry dplyr dqrng easy.utils farver fastmatch filelock FNN generics ggplot2 ggrepel glue gtable h5mread HDF5Array hdf5r hdf5r.Extra HighFive igraph IRanges irlba isoband labeling lattice leidenAlg lifecycle magrittr Matrix MatrixGenerics matrixStats patchwork pbmcapply pillar pkgconfig pROC R6 RANN RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppPlanc RcppProgress rhdf5 rhdf5filters Rhdf5lib rlang RSpectra S4Arrays S4Vectors S7 scales sccore sitmo SparseArray tibble tidyselect utf8 uwot vctrs viridisLite withr XVector

Data integration with LIGER

Introduction | Usage | Loading the package

Rendered fromliger_vignette.Rmdusingknitr::rmarkdown

Last update: 2024-10-29
Started: 2024-10-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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
Align factor loadings to get final integration	alignFactors alignFactors.liger alignFactors.Seurat
Converting other classes of data to a liger object	as.liger as.liger.dgCMatrix as.liger.Seurat as.liger.SingleCellExperiment seuratToLiger
Converting other classes of data to a ligerDataset object	as.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 modality	bmmc
Calculate agreement metric after integration	calcAgreement
Calculate alignment metric after integration	calcAlignment
Calculate adjusted Rand index (ARI) by comparing two cluster labeling variables	calcARI
Calculate a dataset-specificity score for each factor	calcDatasetSpecificity
Calculate Normalized Mutual Information (NMI) by comparing two cluster labeling variables	calcNMI
Calculate purity by comparing two cluster labeling variables	calcPurity
Cell cycle gene set for human	ccGeneHuman
[Experimental] Align factor loading by centroid alignment (beta)	centroidAlign centroidAlign.liger centroidAlign.Seurat
Close all links (to HDF5 files) of a liger object	closeAllH5 closeAllH5.liger closeAllH5.ligerDataset
Check difference of two liger command	commandDiff
Convert old liger object to latest version	convertOldLiger
Access ligerSpatialDataset coordinate data	coordinate coordinate,liger,character-method coordinate,ligerSpatialDataset,missing-method coordinate<- coordinate<-,liger,character-method coordinate<-,ligerSpatialDataset,missing-method
Create on-disk ligerDataset Object	createH5LigerDataset
Create liger object	createLiger
Create in-memory ligerDataset object	createLigerDataset
Data frame for example marker DEG test result	deg.marker
Data frame for example pairwise DEG test result	deg.pw
Downsample datasets	downsample
Line element with fixed length setting	element_line_fixlen
Export predicted gene-pair interaction	exportInteractTrack
Test all factors for enrichment in a gene set	factorGSEA
Find shared and dataset-specific markers	getFactorMarkers
Calculate proportion mitochondrial contribution	getProportionMito
Apply function to chunks of H5 data in ligerDataset object	H5Apply
Import prepared dataset publically available	importBMMC importCGE importPBMC
Impute the peak counts from gene expression data referring to an ATAC dataset after integration	imputeKNN
Check if given liger object if under new implementation	is.newLiger
Check if a liger or ligerDataset object is made of HDF5 file	isH5Liger
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 modality	ligerATACDataset ligerATACDataset-class
ligerCommand object: Record the input and time of a LIGER function call	ligerCommand ligerCommand-class show,ligerCommand-method
ligerDataset class	cbind.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,ligerATACDataset,ANY,missing,missing-method 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 modality	ligerMethDataset ligerMethDataset-class
Subclass of ligerDataset for RNA modality	ligerRNADataset ligerRNADataset-class
Subclass of ligerDataset for Spatial modality	ligerSpatialDataset ligerSpatialDataset-class
Convert between liger and Seurat object	ligerToSeurat
Linking genes to putative regulatory elements	linkGenesAndPeaks
[Superseded] Louvain algorithm for community detection	louvainCluster-deprecated
Fast calculation of feature count matrix	makeFeatureMatrix
[Deprecated] Export predicted gene-pair interaction	makeInteractTrack-deprecated
[Deprecated] Generate a river (Sankey) plot	makeRiverplot-deprecated
Create new variable from categories in cellMeta	mapCellMeta
Merge hdf5 files	mergeH5
Merge matrices while keeping the union of rows	mergeDenseAll mergeSparseAll
Return preset modality of a ligerDataset object or that of all datasets in a liger object	modalOf
[Deprecated] Normalize raw counts data	normalize normalize.DelayedArray normalize.dgCMatrix normalize.liger normalize.ligerDataset normalize.matrix normalize.Seurat normalizePeak
[Deprecated] Perform online iNMF on scaled datasets	online_iNMF-deprecated
[Deprecated] Perform iNMF on scaled datasets	optimizeALS-deprecated
Perform factorization for new data	optimizeNewData
Perform factorization for new value of k	optimizeNewK
Perform factorization for new lambda value	optimizeNewLambda
Perform factorization for subset of data	optimizeSubset
liger object of PBMC subsample data with Control and Stimulated datasets	pbmc
liger object of PBMC subsample data with plotting information available	pbmcPlot
GSEA plot for specific gene set and factor using factorGSEA results	plot.factorGSEA
Create barcode-rank plot for each dataset	plotBarcodeRank
Generate violin/box plot(s) using liger object	plotCellViolin
Make dot plot of factor loading in cell groups	plotClusterFactorDot
Make dot plot of gene expression in cell groups	plotClusterGeneDot
Create violin plot for multiple genes grouped by clusters	plotClusterGeneViolin
Create density plot basing on specified coordinates	plotDensityDimRed
Generate scatter plot(s) using liger object	plotByDatasetAndCluster plotClusterDimRed plotDatasetDimRed plotDimRed plotFactorDimRed plotGeneDimRed plotPeakDimRed
Create volcano plot with EnhancedVolcano	plotEnhancedVolcano
Plot Heatmap of Gene Expression or Factor Loading	plotFactorHeatmap plotGeneHeatmap
Visualize factor expression and gene loading	plotGeneLoadingRank plotGeneLoadings
Visualize gene expression or cell metadata with violin plot	plotGeneDetectedViolin plotGeneViolin plotTotalCountViolin
Visualize GO enrichment test result in dot plot	plotGODot
Comprehensive group splited cluster plot on dimension reduction with proportion	plotGroupClusterDimRed
Create heatmap for showing top marker expression in conditions	plotMarkerHeatmap
Create heatmap for pairwise DEG analysis result	plotPairwiseDEGHeatmap
Visualize proportion across two categorical variables	plotClusterProportions plotProportion plotProportionBar plotProportionDot plotProportionPie
Box plot of cluster proportion in each dataset, grouped by condition	plotProportionBox
Make Riverplot/Sankey diagram that shows label mapping across datasets	plotSankey
Visualize a spatial dataset	plotSpatial2D plotSpatial2D.liger plotSpatial2D.ligerSpatialDataset
Plot the variance vs mean of feature expression	plotVarFeatures
Create volcano plot for Wilcoxon test result	plotVolcano
Show information about factorGSEA object	print.factorGSEA
[Superseded] Quantile align (normalize) factor loading	quantile_norm-deprecated
[Superseded] Quantile align (normalize) factor loadings	quantileAlignSNF
Quantile Align (Normalize) Factor Loadings	quantileNorm quantileNorm.liger quantileNorm.Seurat
Access ligerATACDataset peak data	normPeak 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 10X	read10X read10XATAC read10XRNA
Read 10X cellranger files (matrix, barcodes and features) into R session	read10XFiles
Read 10X HDF5 file	read10XH5 read10XH5Delay read10XH5Mem
Read matrix from H5AD file	readH5AD readH5ADDelay readH5ADMem
Read liger object from RDS file	readLiger
[Superseded] See 'downsample'	readSubset
Remove missing cells or features from liger object	removeMissing removeMissingObs
Restore links (to HDF5 files) for reloaded liger/ligerDataset object	restoreH5Liger restoreOnlineLiger
Retrieve a single matrix of cells from a slot	retrieveCellFeature
Create "scaled data" for DNA methylation datasets	reverseMethData
Perform consensus iNMF on scaled datasets	runCINMF runCINMF.liger runCINMF.Seurat
SNN Graph Based Community Detection	runCluster
General QC for liger object	runGeneralQC
Run Gene Ontology enrichment analysis on differentially expressed genes.	runGOEnrich
Analyze biological interpretations of metagene	runGSEA
Perform iNMF on scaled datasets	runINMF runINMF.liger runINMF.Seurat
Integrate scaled datasets with iNMF or variant methods	runIntegration runIntegration.liger runIntegration.Seurat
Perform online iNMF on scaled datasets	runOnlineINMF runOnlineINMF.liger runOnlineINMF.Seurat
Find DEG between groups	runMarkerDEG runPairwiseDEG runWilcoxon
Perform t-SNE dimensionality reduction	runTSNE
Perform Mosaic iNMF (UINMF) on scaled datasets with unshared features	runUINMF runUINMF.liger
Perform UMAP Dimensionality Reduction	runUMAP
Scale genes by root-mean-square across cells	scaleNotCenter scaleNotCenter.DelayedArray scaleNotCenter.dgCMatrix scaleNotCenter.liger scaleNotCenter.ligerDataset scaleNotCenter.ligerMethDataset scaleNotCenter.Seurat
[Experimental] Batch-aware highly variable gene selection	selectBatchHVG selectBatchHVG.DelayedArray selectBatchHVG.dgCMatrix selectBatchHVG.liger selectBatchHVG.ligerDataset
Select a subset of informative genes	selectGenes selectGenes.liger selectGenes.Seurat
Select variable genes from one dataset with Seurat VST method	selectGenesVST
Subset liger with brackets	sub-liger [.liger
Subset ligerDataset object	sub-ligerDataset [.ligerDataset
Get cell metadata variable	sub-sub-liger [[.liger
Subset liger object	subsetLiger
Subset ligerDataset object	subsetH5LigerDataset subsetLigerDataset subsetMemLigerDataset
[Experimental] Suggest optimal K value for the factorization	suggestK
Show significant results from factorGSEA	summary.factorGSEA
Theme for short-arrow axis like scanpy umap	theme_axis_shortArrow
Update old liger object to up-to-date structure	updateLigerObject
Write in-memory data into H5 file	writeH5 writeH5.default writeH5.dgCMatrix writeH5.liger writeH5.ligerDataset
Write liger object to H5AD files	writeH5AD writeH5AD.dgCMatrix writeH5AD.liger writeH5AD.ligerDataset