Core Utilities for Single-Cell RNA-Seq

[Up] [Top]

Documentation for package ‘sccore’ version 1.0.1

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
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 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
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)