Man pages for YosefLab/VISION
Functional interpretation of single cell RNA-seq latent manifolds
| addHotspotToVision | Add HS python obj to vision OBJECT |
| addLatentSpace | Add a latent space computed using an external method |
| addProjection-Vision-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 |
| analyzeHotspotObjectVision | Analyze a Hotspot object using built in methods such such as... |
| analyzeLocalCorrelations | Compute local correlations for all signatures |
| analyzeLocalCorrelationsModules | Compute local correlations for all modules |
| analyzeTrajectoryCorrelations | Compute trajectory correlations for all signatures |
| analyze-Vision-method | Main entry point for running VISION Analysis |
| ancestor_at_depth | Find the ancestor of a node above a specific depth |
| annotateLatentComponents | Compute pearson correlation between signature scores and... |
| applyFilters | Applies filters to the inputted expression data (may remove... |
| 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... |
| applyRBFPCA | Performs PCA on data that has been transformed with the... |
| 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 |
| batchify | Utility methods Helper utility to group list items into... |
| batchSigEvalNorm | Evaluate signature scores efficiently in batches |
| calcInterEdgeDistMat | Calculate all distances between points on two different edges |
| calcIntraEdgeDistMat | Calculate distances between all points on a given edge,... |
| calc_mod_sig_enrichment | Computes the hypergeometric overlap test for modules and... |
| calcModuleScores | Calculate module scores (signature scores but on the modules) |
| calc_set_enrichment | Calculate the hypergeometric enrichment for two sets from a... |
| calcSignatureScores | calculate signature scores |
| calculateTrajectoryDistances | Calculate distance matrix between all pairs of ponts based on... |
| 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... |
| clusterCells | Creates clustering of the cells |
| clusterModScores | Compute Ranksums Test, for all factor meta data. One level... |
| clusterSignatures | Clusters signatures according to the rank sum |
| clusterSigScores | Compute Ranksums Test, for all factor meta data. One level... |
| colNormalization | Performs z-normalization on all columns |
| colRankNormalization | Creaes a new version of the data that has ranks (column-wise)... |
| colVarsSp | Compute col-wise variance on matrix without densifying |
| computeKNNWeights-matrix-method | compute for each vector the weights to apply to it's K... |
| computeKNNWeights-phylo-method | Compute for each vector the weights to apply to it's K... |
| computeKNNWeights-Trajectory-method | Compute KNN weights based on geodesic distances for... |
| 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... |
| createGeneSignature | Create a user-defined gene signature |
| createTrajectoryMetaData | Generate meta-data associated with this trajectory |
| depthBasedCladewiseTreeCluster | Performs a breadth first search to create a specific number... |
| depthBasedTreeCluster | Performs a binary search on a depth d such that if... |
| dot-colNormHelper | Calculates the column znormalization after row znormalization |
| draw_hotspot_heatmap | Draw Modules Heatmap (Gene x Gene) |
| evalSigGeneImportance | Calculate gene-signature importance |
| evalSigGeneImportanceSparse | Calculate Gene-Signature Importance |
| 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... |
| filterGenesThreshold | Filter genes whose values sum to less than some threshold... |
| find_knn_parallel | Parallel KNN |
| find_knn_parallel_tree | Parallel KNN for Trees |
| find_root | Find the root node |
| fitTree | Fit tree using input parameters |
| geary_sig_v_proj | Evaluates values vs coordinates using the Geary C |
| generateOverlapSignatures | Generates signature objects for the overlap sets between... |
| generatePermutationNull | Generate random signatures for a null distribution by... |
| generateProjections | generate projections |
| generateProjectionsInner | Projects data into 2 dimensions using a variety of linear and... |
| generateTrajectoryProjections | Generate 2d representations of a trajectory model |
| get_all_children | Get all the tip children of a node. |
| get_children | Find the children of a node |
| getLatentSpace | Get Latent Space |
| getLatentTrajectory | Get Latent Trajectory |
| get_max_cluster_size | Tree method for getting the max child clade size of a node |
| getMetaAutocorrelation | Get MetaData Autocorrelation Scores |
| getMetaDifferential | Get Results of One-vs-All Differential Tests with Metadata... |
| get_min_cluster_size | Tree method for getting the min child clade size of a node |
| 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 |
| get_parent | Get the parent of a node |
| getProjections | Get 2D views of the expression data |
| getSelections | Get saved selections |
| getSignatureAutocorrelation | Get Signature Autocorrelation Scores |
| getSignatureDifferential | Get Results of One-vs-All Differential Signature Tests |
| getSignatureScores | Get Signature Scores |
| group_modules_enrichment | Make the clusters for the modules by enrichment. For now we... |
| hasUnnormalizedData | Tests for Unnormalized Data |
| hsCalculateModuleScores | Create Hotspot Modules and calculate module scores given a HS... |
| hsComputeAutoCorrelations | Compute Hotspot auto correlations |
| hsComputeLocalCorrelations | Interface function to compute local correlations for Hotspot... |
| hsCreateKnnGraph | Init KNN graph in Hotspot object |
| hsInit | Init Hotspot object from Vision Object |
| ilog1p | inverse log-scale transform a dense OR sparse matrix |
| innerEvalSignatureBatchNorm | Used in inner loop of batchSigEvalNorm |
| is_tip | Check if a child is a tip |
| knn_tree | Helper KNN Function for Trees |
| launchServer | Lanch the server |
| lca_based_depth | Depth of tip1 parent immediately after LCA(tip1, tip2) |
| lcaBasedHotspotNeighbors | Add custom tree based neighbor and weights to a Hotspot... |
| lcaBasedTreeKNN | Generate neighbors and weights for a tree object, based on... |
| loadHotspotObject | Load in an existing Hotspot object from bytes or a file |
| louvainCluster | Applies the Louvain algorithm to generate micro-clustered... |
| matLog2 | log2-scale transform a dense OR sparse matrix |
| matrix_chisq | Perform 1vAll factor analysis given a factor matrix and group... |
| matrix_wilcox | Vectorized wilcox rank-sums test |
| matrix_wilcox_cpp | C++ wilcox rank-sums test |
| maxSizeCladewiseTreeCluster | Performs a breadth first search to create a specific number... |
| minSizeCladeNeighbors | Get's the nearest >= min size neighbors of a node based on... |
| noNormalization | Does nothing, just returns the original data |
| NormData | Initialize a new NormData object |
| pearsonCorrToJSON | convert perason correlation coeffcients between PCs and... |
| phyloAnalyze-PhyloVision-method | Analyze a PhyloVision object |
| PhyloVision-class | Initializes a new PhyloVision Object |
| poolCells | create micro-clusters that reduce noise and complexity while... |
| 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... |
| 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 |
| readjust_clusters | Repartitions existing clusters to achieve desired... |
| readSignaturesInput | Reads in a list of signature input files. |
| 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 |
| runHotspot | Perform Hotspot analysis on Vision Object |
| saveAndViewResults-Vision-method | Save the VISION object as an .RDS file and view the results... |
| saveHSBytestToPickle | Save bytes in the Hotspot object slot to a file |
| 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 signatures 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... |
| sigsVsProjection_pcf | Evaluates the significance of each meta data factor signature... |
| sigsVsProjection_pcn | Evaluates the significance of each meta data numeric... |
| sqdist | Alternative computation of distance matrix, based on matrix... |
| Trajectory | Initialize a new Trajectory object. |
| TrajectoryProjection | Initialize a new TrajectoryProjection object. |
| translateCellPositions | Translate cell positions |
| treeClusterMinCladeSize | Generate clade-clusters for a tree of minimum size (unless... |
| trivial_dist | Trivial distance function for arbitrary tree clustering |
| ultrametric_tree | Generate an ultrametric tree |
| versionCheck | Checks the version of the Vision object and displays error if... |
| viewResults | View results of analysis |
| VISION | VISION |
| VISION-class | Initializes a new VISION object. |
