# Functional interpretation of single cell RNA-seq latent manifolds

## Documentation for package ‘VISION’ version 2.0.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C E F G H I L M N P R S T V misc

VISION-package | VISION

## -- A --

addLatentSpace | Add a latent space computed using an external method
addProjection | Add a set of projection coordinates to use for visualization
addProjection-method | Add a set of projection coordinates to use for visualization
addSignatures | Add signatures to VISION object
addTSNE | Adds a tSNE projection
addUMAP | Adds a UMAP projection
analyze | Main entry point for running VISION Analysis
analyze-method | Main entry point for running VISION Analysis
analyzeLocalCorrelations | Compute local correlations for all signatures
analyzeTrajectoryCorrelations | Compute trajectory correlations for all signatures
annotateLatentComponents | Compute pearson correlation between signature scores and components of the Latent Space
applyFilters | Applies filters to the inputted expression data (may remove rows)
applyICA | Performs ICA on data
applyISOMap | Performs ISOMap on data
applyMicroClustering | Pool cells into microclusters
applyPCA | Performs PCA on data
applyPermutationWPCA | Applies pemutation method to return the most significant components of PCA data
applyRBFPCA | Performs PCA on data that has been transformed with the Radial Basis Function.
applySimplePPT | Applies the Simple PPT algorithm onto the expression data.
applySpectralEmbedding | Performs Spectral Embedding on data
applytSNE10 | Performs tSNE with perplexity 10 on data
applytSNE30 | Performs tSNE with perplexity 30 on data
applyUMAP | Performs UMAP on data

## -- B --

batchify | Utility methods Helper utility to group list items into batches
batchSigEvalNorm | Evaluate signature scores efficiently in batches

## -- C --

calcInterEdgeDistMat | Calculate all distances between points on two different edges
calcIntraEdgeDistMat | Calculate distances between all points on a given edge, including edge vertices
calcSignatureScores | calculate signature scores
calculateTrajectoryDistances | Calculate distance matrix between all pairs of ponts based on their projection onto the tree
clipBottom | Sets all values below a certain level in the data equal to 0
Cluster | Wrapper class for a particular cluster. Maps a cluster type to the the resulting cluster data.
clusterCells | Creates clustering of the cells
clusterSignatures | Clusters signatures according to the rank sum
clusterSigScores | Compute Ranksums Test, for all factor meta data. One level vs all others
colNormalization | Performs z-normalization on all columns
colRankNormalization | Creaes a new version of the data that has ranks (column-wise) instead of values.
colVarsSp | Compute col-wise variance on matrix without densifying
computeKNNWeights-method | Compute KNN weights based on geodesic distances for Trajectory objects
computeKNNWeights-method | compute for each vector the weights to apply to it's K nearest neighbors
computeLatentSpace | Computes the latent space of the expression matrix using PCA
computeProjectionGenes | filter data accourding to the provided filters
convertGeneIds | Change Gene Identifiers
coordinatesToJSON | Converts a projection into a JSON object mapping each sample to a projection coordinate.
createGeneSignature | Create a user-defined gene signature
createTrajectoryMetaData | Generate meta-data associated with this trajectory

## -- E --

evalSigGeneImportance | Calculate gene-signature importance
evalSigGeneImportanceSparse | Calculate Gene-Signature Importance

## -- F --

fbConsistencyScores | Evaluates the significance of each protein
filterGenesFano | Applies the Fano filter to the input data (may remove rows)
filterGenesNovar | Eliminate genes whose sample variance is equal to 0 (may remove rows); run when -nofilter option is selected
filterGenesThreshold | Filter genes whose values sum to less than some threshold value (may remove rows)
find_knn_parallel | Parallel KNN
fitTree | Fit tree using input parameters

## -- G --

geary_sig_v_proj | Evaluates values vs coordinates using the Geary C
generatePermutationNull | Generate random signatures for a null distribution by permuting the data
generateProjections | generate projections
generateProjectionsInner | Projects data into 2 dimensions using a variety of linear and non-linear methods.
generateTrajectoryProjections | Generate 2d representations of a trajectory model
getLatentSpace | Get Latent Space
getLatentSpace-method | Get Latent Space
getLatentTrajectory | Get Latent Trajectory
getLatentTrajectory-method | Get Latent Trajectory
getMetaAutocorrelation | Get MetaData Autocorrelation Scores
getMetaAutocorrelation-method | Get MetaData Autocorrelation Scores
getMetaDifferential | Get Results of One-vs-All Differential Tests with Metadata Variables
getMetaDifferential-method | Get Results of One-vs-All Differential Tests with Metadata Variables
getMSE | Calculates the MSE between C and X
getNormalizedCopy | Calculates the specified normalized data matrix
getNormalizedCopySparse | Calculates the specified normalized data matrix
getParam | Gets parameters with defaults
getProjections | Get 2D views of the expression data
getProjections-method | Get 2D views of the expression data
getSelections | Get saved selections
getSelections-method | Get saved selections
getSignatureAutocorrelation | Get Signature Autocorrelation Scores
getSignatureAutocorrelation-method | Get Signature Autocorrelation Scores
getSignatureDifferential | Get Results of One-vs-All Differential Signature Tests
getSignatureDifferential-method | Get Results of One-vs-All Differential Signature Tests
getSignatureScores | Get Signature Scores
getSignatureScores-method | Get Signature Scores

## -- H --

hasUnnormalizedData | Tests for Unnormalized Data

## -- I --

ilog1p | inverse log-scale transform a dense OR sparse matrix
innerEvalSignatureBatchNorm | Used in inner loop of batchSigEvalNorm

## -- L --

launchServer | Lanch the server
louvainCluster | Applies the Louvain algorithm to generate micro-clustered data

## -- M --

matLog2 | log2-scale transform a dense OR sparse matrix
matrix_chisq | Perform 1vAll factor analysis given a factor matrix and group definition
matrix_wilcox | Vectorized wilcox rank-sums test
matrix_wilcox_cpp | C++ wilcox rank-sums test

## -- N --

noNormalization | Does nothing, just returns the original data
NormData | Initialize a new NormData object

## -- P --

pearsonCorrToJSON | convert perason correlation coeffcients between PCs and sgnatures into a JSON object
poolCells | create micro-clusters that reduce noise and complexity while maintaining the overall signal in the data
poolMatrixCols | Pools columns of a numeric matrix
poolMatrixCols_Inner | create "super-cells" by pooling together single cells
poolMatrixRows | Pools rows of a numeric matrix
poolMetaData | Aggregate meta-data for cells in pools
processSignatures | Processes signatures on input
projectOnTree | Project the given dataoints onto the tree defined by the vertices (V.pos) and binary adjacency matrix (princAdj)

## -- R --

readjust_clusters | Repartitions existing clusters to achieve desired granularity.
readSignaturesInput | Reads in a list of signature input files.
read_10x | Read 10x Output
read_10x_h5 | Read 10x HDF5 Output
read_10x_h5_v2 | Read 10x HDF5 Output - CellRanger 2.0
read_10x_h5_v3 | Read 10x HDF5 Output - CellRanger 3.0
registerMethods | Registers the projection methods to be used
rowAndColNormalization | Performs z-normalization on all columns and rows
rowNormalization | Performs z-normalization on all rows
rowVarsSp | Compute row-wise variance on matrix without densifying

## -- S --

saveAndViewResults | Save the VISION object as an .RDS file and view the results on a localhost
saveAndViewResults-method | Save the VISION object as an .RDS file and view the results on a localhost
ServerExpression | Wrapper class for gene expression object for JSON.
ServerSigProjMatrix | Wrapper class for Signature Projection Matrix
sigConsistencyScores | Evaluates the significance of each signature in each cluster
Signature | Initialize a new Signature object.
signatureToJSON | Converts Signature object to JSON
sigProjMatrixToJSON | Converts a sigProjMatrix from an R Object to a JSON object
sigScoresToJSON | Converts row of sigantures score matrix to JSON
sigsToSparseMatrix | Utility method to load signatures into a sparse matrix
sigsVsProjection_n | Evaluates the significance of each numeric signature vs. a single projections weights
sigsVsProjection_pcf | Evaluates the significance of each meta data factor signature vs. a single projections weights
sigsVsProjection_pcn | Evaluates the significance of each meta data numeric signature vs. a single projections weights
sqdist | Alternative computation of distance matrix, based on matrix multiplication.

## -- T --

Trajectory | Initialize a new Trajectory object.
TrajectoryProjection | Initialize a new TrajectoryProjection object.
translateCellPositions | Translate cell positions

## -- V --

versionCheck | Checks the version of the Vision object and displays error if necessary
viewResults | View results of analysis
viewResults-method | View results of analysis
VISION | VISION
Vision | Initializes a new VISION object.
Vision-method | Initializes a new VISION object.

## -- misc --

.colNormHelper | Calculates the column znormalization after row znormalization