# Core Utilities for Single-Cell RNA-Seq

## Documentation for package ‘sccore’ version 1.0.6

- DESCRIPTION file.

## Help Pages

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
checkPackageInstalled | Check whether a package is installed and suggest how to install from CRAN, Bioconductor, or other external source
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
colSumByFactor | Calculates factor-stratified sums for each column
conosClusterList | Conos clusters list
conosGraph | Conos graph
dotPlot | Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot for details
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 | embeddingPlot generic Plot embedding with provided labels / colors using ggplot2
embeddingPlot-method | embeddingPlot generic Plot embedding with provided labels / colors using ggplot2
embeddingPlot-methods,ANY | embeddingPlot generic Plot embedding with provided labels / colors using ggplot2
embeddingPlot-methods,Seurat | embeddingPlot generic Plot embedding with provided labels / colors using ggplot2
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.
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
saveDeAsJson | Save DE results as JSON tables for viewing in browser
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)