adjacentVertices        List of adjacent vertices from igraph object
adjacent_vertex_weights
                        List of adjacent vertex weights from igraph
                        object
appendSpecificityMetricsToDE
                        Append specificity metrics to DE
as_factor               convert character vector into a factor with
                        names "values" and "levels"
cellAnnotations         Conos cell annotations
colSumByFactor          Calculates factor-stratified sums for each
                        column
collapseCellsByType     Collapse count matrices by cell type, given
                        min/max number of cells
collapseGraphPaga       Collapse graph using PAGA 1.2 algorithm, Wolf
                        et al 2019, Genome Biology (2019)
                        <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x>
collapseGraphSum        Collapse Graph By Sum
conosClusterList        Conos clusters list
conosGraph              Conos graph
dotPlot                 Dot plot adapted from Seurat:::DotPlot, see
                        ?Seurat:::DotPlot for details
embedGraphUmap          Embed a graph into a UMAP, Uniform Manifold
                        Approximation and Projection for Dimension
                        Reduction, <https://github.com/lmcinnes/umap>,
                        <doi:10.21105/joss.00861>
embedKnnGraph           Embed a k-nearest neighbor (kNN) graph within a
                        UMAP. Used within embedGraphUmap(). Please see
                        McInnes et al <doi:10.21105/joss.00861> for the
                        UMAP description and implementation.
embeddingColorsPlot     Set colors for embedding plot. Used primarily
                        in embeddingPlot().
embeddingGroupPlot      Plotting function for cluster labels, names
                        contain cell names. Used primarily in
                        embeddingPlot().
embeddingPlot           Plot embedding with provided labels / colors
                        using ggplot2
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 palettes. Used primarily within
                        embeddingGroupPlot()
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 / lambda_m - a|^b)
jsDist                  Jensen–Shannon distance metric (i.e. the square
                        root of the Jensen–Shannon divergence) between
                        the columns of a dense matrix m
mergeCountMatrices      Merge list of count matrices into a common
                        matrix, entering 0s for the missing entries
multi2dend              Translate multilevel segmentation into a
                        dendrogram, with the lowest level of the
                        dendrogram listing the cells
plapply                 Parallel, optionally verbose lapply. See
                        ?parallel::mclapply for more info.
propagateLabels         Estimate labeling distribution for each vertex,
                        based on provided labels.
propagateLabelsDiffusion
                        Estimate labeling distribution for each vertex,
                        based on provided labels using a Random Walk on
                        graph
propagateLabelsSolver   Propagate labels using Zhu, Ghahramani,
                        Lafferty (2003) algorithm, "Semi-Supervised
                        Learning Using Gaussian Fields and Harmonic
                        Functions"
                        <http://mlg.eng.cam.ac.uk/zoubin/papers/zgl.pdf>
propagate_labels        Label propagation
setMinMax               Set range for values in object. Changes values
                        outside of range to min or max. Adapted from
                        Seurat::MinMax
smoothSignalOnGraph     Smooth Signal on Graph
smooth_count_matrix     Smooth gene expression, used primarily within
                        conos::correctGenes. Used to smooth gene
                        expression values in order to better represent
                        the graph structure. Use diffusion of
                        expression on graph with the equation dv =
                        exp(-a * (v + b))
sn                      Set names equal to values, a stats::setNames
                        wrapper function
splitVectorByNodes      splitVectorByNodes
styleEmbeddingPlot      Set plot.theme, legend, ticks for embedding
                        plot. Used primarily in embeddingPlot().
umapEmbedding           UMAP embedding
val2col                 Utility function to translate values into
                        colors.
val2ggcol               Helper function to return a ggplot color
                        gradient for a numeric vector
                        ggplot(aes(color=x, ...), ...) + val2ggcol(x)
