| adjacent_vertex_weights | List of adjacent vertex weights from igraph object |
| adjacentVertices | List of adjacent vertices from igraph object |
| appendSpecificityMetricsToDE | Append specificity metrics to DE |
| as_factor | convert character vector into a factor with names "values"... |
| cellAnnotations | Conos cell annotations |
| checkPackageInstalled | Check whether a package is installed and suggest how to... |
| collapseCellsByType | Collapse count matrices by cell type, given min/max number of... |
| collapseGraphPaga | Collapse graph using PAGA 1.2 algorithm, Wolf et al 2019,... |
| collapseGraphSum | Collapse Graph By Sum |
| colSumByFactor | Calculates factor-stratified sums for each column |
| computeChebyshevCoeffs | Compute Chebyshev Coefficients |
| conosClusterList | Conos clusters list |
| conosGraph | Conos graph |
| dotPlot | Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot... |
| embeddingColorsPlot | Set colors for embedding plot. Used primarily in... |
| embeddingGroupPlot | Plotting function for cluster labels, names contain cell... |
| embeddingPlot | Plot embedding with provided labels / colors using ggplot2 |
| embedGraphUmap | Embed a graph into a UMAP, Uniform Manifold Approximation and... |
| embedKnnGraph | Embed a k-nearest neighbor (kNN) graph within a UMAP. Used... |
| extendMatrix | Extend matrix to include new columns in matrix |
| fac2col | Utility function to translate a factor into colors |
| fac2palette | Encodes logic of how to handle named-vector and functional... |
| getClusterGraph | Collapse vertices belonging to each cluster in a graph |
| get_nearest_neighbors | Get nearest neighbors method on graph |
| graphToAdjList | Convert igraph graph into an adjacency list |
| heatFilter | Graph filter with the heat kernel: f(x) = exp(-beta |x /... |
| jsDist | Jensen–Shannon distance metric (i.e. the square root of the... |
| mergeCountMatrices | Merge list of count matrices into a common matrix, entering... |
| multi2dend | Translate multilevel segmentation into a dendrogram, with the... |
| plapply | Parallel, optionally verbose lapply. See ?parallel::mclapply... |
| propagate_labels | Label propagation |
| propagateLabels | Estimate labeling distribution for each vertex, based on... |
| propagateLabelsDiffusion | Estimate labeling distribution for each vertex, based on... |
| propagateLabelsSolver | Propagate labels using Zhu, Ghahramani, Lafferty (2003)... |
| saveDeAsJson | Save DE results as JSON tables for viewing in browser |
| setMinMax | Set range for values in object. Changes values outside of... |
| smoothChebyshev | Smooth with Chebyshev Polynomials |
| smooth_count_matrix | Smooth gene expression, used primarily within... |
| smoothSignalOnGraph | Smooth Signal on Graph |
| sn | Set names equal to values, a stats::setNames wrapper function |
| splitVectorByNodes | splitVectorByNodes |
| styleEmbeddingPlot | Set plot.theme, legend, ticks for embedding plot. Used... |
| umapEmbedding | UMAP embedding |
| val2col | Utility function to translate values into colors. |
| val2ggcol | Helper function to return a ggplot color gradient for a... |
