Function reference • ArchR

Arrow file creation Functions that help create / set up an ArrowFile
`createArrowFiles()`	Create Arrow Files
`createGenomeAnnotation()`	Create a genome annotation object for ArchR
`filterDoublets()`	Filter Doublets From an ArchRProject
`nCells()`	Get the number of cells from an ArchRProject/ArrowFile
`reformatFragmentFiles()`	Reformat Fragment Files to be Tabix and Chr Sorted
Add-ers Functions that add information to ArrowFiles or an ArchRProject
`addArchRAnnotations()`	Add ArchR annotations to an ArchRProject
`addArchRChrPrefix()`	Add a globally-applied requirement for chromosome prefix
`addArchRDebugging()`	Set ArchR Debugging
`addArchRGenome()`	Add a globally defined genome to all ArchR functions.
`addArchRLogging()`	Set ArchR Logging
`addArchRThreads()`	Add a globally-applied number of threads to use for parallel computing.
`addArchRVerbose()`	Set ArchR Verbosity for Log Messaging
`addBgdPeaks()`	Add Background Peaks to an ArchRProject
`addCellColData()`	Add information to cellColData in an ArchRProject
`addClusters()`	Add cluster information to an ArchRProject
`addCoAccessibility()`	Add Peak Co-Accessibility to an ArchRProject
`addCombinedDims()`	Combine two or more modalities dimensionality reductions.
`addDemuxletResults()`	Add Demuxlet Results to ArchR Project
`addDeviationsMatrix()`	Add a matrix of deviations for a given peakAnnotation to Arrow Files in ArchRProject
`addDoubletScores()`	Add Doublet Scores to a collection of ArrowFiles or an ArchRProject
`addFeatureCounts()`	This function will add total counts of scATAC cells in provided features into ArchRProject.
`addFeatureMatrix()`	Add a feature matrix to an ArchRProject or a set of ArrowFiles
`addGeneExpressionMatrix()`	Add Gene Expression Matrix to ArrowFiles or an ArchRProject
`addGeneIntegrationMatrix()`	Add a GeneIntegrationMatrix to ArrowFiles or an ArchRProject
`addGeneScoreMatrix()`	Add GeneScoreMatrix to ArrowFiles or an ArchRProject
`addGroupCoverages()`	Add Group Coverages to an ArchRProject object
`addHarmony()`	Add Harmony Batch Corrected Reduced Dims to an ArchRProject
`addImputeWeights()`	Add Imputation Weights to an ArchRProject
`addIterativeLSI()`	Add an Iterative LSI-based dimensionality reduction to an ArchRProject
`addModuleScore()`	Add Module Scores to an ArchRProject
`addMonocleTrajectory()`	Add a Monocle Trajectory to an ArchR Project #NEW
`addMotifAnnotations()`	Add motif annotations to an ArchRProject
`addPeak2GeneLinks()`	Add Peak2GeneLinks to an ArchRProject
`addPeakAnnotations()`	Add peak annotations to an ArchRProject
`addPeakMatrix()`	Add a Peak Matrix to the ArrowFiles of an ArchRProject
`addPeakSet()`	Add a peak set to an ArchRProject
`addProjectSummary()`	Add projectSummary to an ArchRProject
`addReproduciblePeakSet()`	Add a Reproducible Peak Set to an ArchRProject
`addSampleColData()`	Add information to sampleColData in an ArchRProject
`addSlingShotTrajectories()`	Add a Slingshot Trajectories to an ArchR Project #NEW
`addTSNE()`	Add a TSNE embedding of a reduced dimensions object to an ArchRProject
`addTileMatrix()`	Add TileMatrix to ArrowFiles or an ArchRProject
`addTrajectory()`	Add a Supervised Trajectory to an ArchR Project
`addUMAP()`	Add a UMAP embedding of a reduced dimensions object to an ArchRProject
Get-ers Functions that get information from ArrowFiles or an ArchRProject
`getArchRChrPrefix()`	Get a globally-applied requirement for chromosome prefix
`getArchRDebugging()`	Get ArchR Debugging
`getArchRGenome()`	Get the globally defined genome, the geneAnnotation, or genomeAnnotation objects associated with the globally defined genome.
`getArchRLogging()`	Get ArchR Logging
`getArchRThreads()`	Get globally-applied number of threads to use for parallel computing.
`getArchRVerbose()`	Set ArchR Verbosity for Log Messaging
`getArrowFiles()`	Get ArrowFiles from an ArchRProject
`getAvailableMatrices()`	Get a list available matrices in the ArrowFiles storted in an ArchRProject
`getBgdPeaks()`	Get Background Peaks from an ArchRProject
`getBlacklist()`	Get the blacklist from an ArchRProject
`getCellColData()`	Get cellColData from an ArchRProject
`getCellNames()`	Get cellNames from an ArchRProject
`getChromLengths()`	Get chromLengths from ArchRProject
`getChromSizes()`	Get chromSizes from ArchRProject
`getCoAccessibility()`	Get the peak co-accessibility from an ArchRProject
`getEmbedding()`	Get embedding information stored in an ArchRProject
`getExons()`	Get the exons from an ArchRProject
`getFeatures()`	Get the features that could be selected from a given data matrix within an ArchRProject
`getFootprints()`	Calculate footprints from an ArchRProject
`getFragmentsFromArrow()`	Get the fragments from an ArrowFile
`getFragmentsFromProject()`	Get the fragments from an ArchRProject
`getGeneAnnotation()`	Get geneAnnotation from an ArchRProject
`getGenes()`	Get the genes from an ArchRProject
`getGenome()`	Get the genome used by an ArchRProject
`getGenomeAnnotation()`	Get the genomeAnnotation from an ArchRProject
`getGroupBW()`	Export Group BigWigs
`getGroupSE()`	Export Group Summarized Experiment
`getGroupSummary()`	Get summary for Groups in ArchRProject
`getImputeWeights()`	Get Imputation Weights from ArchRProject
`getInputFiles()`	Get Input Files from paths to create arrows
`getMarkerFeatures()`	Identify Marker Features for each cell grouping
`getMarkers()`	Get Marker Features from a marker summarized experiment
`getMatches()`	Get peak annotation matches from an ArchRProject
`getMatrixFromArrow()`	Get a data matrix stored in an ArrowFile
`getMatrixFromProject()`	Get a data matrix stored in an ArchRProject
`getMonocleTrajectories()`	Get a Monocle CDS of Trajectories that can be added to an ArchRProject #NEW
`getOutputDirectory()`	Get outputDirectory from an ArchRProject
`getPeak2GeneLinks()`	Get the peak-to-gene links from an ArchRProject
`getPeakAnnotation()`	Get peakAnnotation from an ArchRProject
`getPeakSet()`	Get the peak set from an ArchRProject
`getPositions()`	Get peak annotation positions from an ArchRProject
`getProjectSummary()`	Get projectSummary from an ArchRProject
`getReducedDims()`	Get dimensionality reduction information stored in an ArchRProject
`getSampleColData()`	Get sampleColData from an ArchRProject
`getSampleNames()`	Get the sample names from an ArchRProject
`getSeqnames()`	Get the seqnames that could be selected from a given data matrix within an ArchRProject
`getTSS()`	Get the transcription start sites of all genes in an ArchRProject
`getTestFragments()`	Get PBMC Small Test Fragments
`getTestProject()`	Get PBMC Small Test Project
`getTrajectory()`	Get Supervised Trajectory from an ArchR Project
`getTutorialData()`	Get Relevant Data For ArchR Tutorials
`getValidBarcodes()`	Get Valid Barcodes from 10x Cell Ranger output to pre-filter barcodes
`getVarDeviations()`	Get Variable Deviations across cells in ArchRProject.
Manipulating an ArchRProject Functions for manipulating an ArchRProject
`ArchRProject()`	Create ArchRProject from ArrowFiles
`loadArchRProject()`	Load Previous ArchRProject into R
`recoverArchRProject()`	Recover ArchRProject if broken sampleColData/cellColData
`saveArchRProject()`	Save ArchRProject for Later Usage
`subsetArchRProject()`	Subset an ArchRProject for downstream analysis
`subsetCells()`	Subset cells in an ArchRProject.
Plotting / aesthetic functions Functions for plotting in ArchR
`ArchRBrowser()`	Launch ArchR Genome Browser
`ArchRPalettes`	List of color palettes that can be used in plots
`ggAlignPlots()`	Align ggplot plots vertically or horizontally
`ggGroup()`	A ggplot-based ridge/violin plot wrapper function
`ggHex()`	A ggplot-based Hexplot wrapper function summary of points in a standardized manner
`ggOneToOne()`	A ggplot-based one-to-one dot plot wrapper function
`ggPoint()`	A ggplot-based dot plot wrapper function
`paletteContinuous()`	Continuous Color Palette
`paletteDiscrete()`	Optimized discrete color palette generation
`plotBrowserTrack()`	Plot an ArchR Region Track
`plotEmbedding()`	Visualize an Embedding from ArchR Project
`plotEnrichHeatmap()`	Plot a Heatmap of Peak Annotation Hypergeometric Enrichment in Marker Peaks.
`plotFootprints()`	Plot Footprints
`plotFragmentSizes()`	Plot the fragment size distribution for each sample
`plotGroups()`	Visualize Groups from ArchR Project
`plotMarkerHeatmap()`	Plot a Heatmap of Identified Marker Features
`plotMarkers()`	Plot Differential Markers
`plotPDF()`	Plot PDF in outputDirectory of an ArchRProject
`plotPeak2GeneHeatmap()`	Plot Peak2Gene Heatmap from an ArchRProject
`plotTSSEnrichment()`	Plot a TSS Enrichment Plot for Each Sample
`plotTrajectory()`	Visualize a Trajectory from ArchR Project
`plotTrajectoryHeatmap()`	Plot a Heatmap of Features across a Trajectory
`theme_ArchR()`	ggplot2 default theme for ArchR
Helper functions Functions that make things easier
`%ni%`	Negated Value Matching
`%bcin%`	Generic matching function for S4Vector objects
`%bcni%`	Negated matching function for S4Vector objects
`createLogFile()`	Create a Log File for ArchR
`findMacs2()`	Find the installed location of the MACS2 executable
`installExtraPackages()`	Install extra packages used in ArchR that are not installed by default
`validBSgenome()`	Get/Validate BSgenome
GRanges manipulation Functions to manipulate GRanges objects
`extendGR()`	Extend regions from a Genomic Ranges object
`filterChrGR()`	Filters unwanted seqlevels from a Genomic Ranges object or similar object
`nonOverlappingGR()`	Retreive a non-overlapping set of regions from a Genomic Ranges object
Other ArchR Functions Functions that didnt fit into one of the above categories
`confusionMatrix()`	Create a Confusion Matrix based on two value vectors
`correlateMatrices()`	Correlate Matrices within an ArchRProject
`correlateTrajectories()`	Correlate Trajectories
`imputeMatrix()`	Impute a matrix with impute weights
`mapLabels()`	Re-map a character vector of labels from an old set of labels to a new set of labels
`peakAnnoEnrichment()`	Peak Annotation Hypergeometric Enrichment in Marker Peaks.
`projectBulkATAC()`	Project Bulk ATAC-seq data into single cell subspace

Reference

Arrow file creation

Add-ers

Get-ers

Manipulating an ArchRProject

Plotting / aesthetic functions

Helper functions

GRanges manipulation

Other ArchR Functions