Reference

Primary methods
Vision()	Initializes a new VISION object.
analyze(<Vision>)	Main entry point for running VISION Analysis
viewResults(<Vision>) viewResults(<character>)	View results of analysis
Customizing VISION
addProjection(<Vision>)	Add a set of projection coordinates to use for visualization
createGeneSignature()	Create a user-defined gene signature
Accessing Data inside the VISION object
getSignatureScores(<Vision>)	Get Signature Scores
getLatentSpace(<Vision>)	Get Latent Space
getLatentTrajectory(<Vision>)	Get Latent Trajectory
getProjections(<Vision>)	Get 2D views of the expression data
getSignatureAutocorrelation(<Vision>)	Get Signature Autocorrelation Scores
getMetaAutocorrelation(<Vision>)	Get MetaData Autocorrelation Scores
getSignatureDifferential(<Vision>)	Get Results of One-vs-All Differential Signature Tests
getMetaDifferential(<Vision>)	Get Results of One-vs-All Differential Tests with Metadata Variables
getSelections(<Vision>)	Get saved selections
Micropooling
applyMicroClustering()	Pool cells into microclusters
poolMatrixCols()	Pools columns of a numeric matrix
poolMatrixRows()	Pools rows of a numeric matrix
poolMetaData()	Aggregate meta-data for cells in pools
PhyloVision
PhyloVision()	Initializes a new PhyloVision Object
phyloAnalyze(<PhyloVision>)	Analyze a PhyloVision object
Hotspot
runHotspot()	Perform Hotspot analysis on Vision Object
hsInit()	Init Hotspot object from Vision Object
hsCreateKnnGraph()	Init KNN graph in Hotspot object
hsComputeAutoCorrelations()	Compute Hotspot auto correlations
hsComputeLocalCorrelations()	Interface function to compute local correlations for Hotspot Warning: modifies the hs argument
hsCalculateModuleScores()	Create Hotspot Modules and calculate module scores given a HS object with local correlations already calculated
analyzeHotspotObjectVision()	Analyze a Hotspot object using built in methods such such as local correlation, signature overlap, etc. Necessary to run this function for Hotspot functionality in viewer to work.
loadHotspotObject()	Load in an existing Hotspot object from bytes or a file
draw_hotspot_heatmap()	Draw Modules Heatmap (Gene x Gene)
Miscellaneous
convertGeneIds()	Change Gene Identifiers
read_10x()	Read 10x Output
read_10x_h5()	Read 10x HDF5 Output