Core Utilities for Single-Cell RNA-Seq
List of adjacent vertex weights from igraph object
List of adjacent vertices from igraph object
Append specificity metrics to DE
convert character vector into a factor with names "values" and "levels...
Check whether a package is installed and suggest how to install from C...
Collapse count matrices by cell type, given min/max number of cells
Collapse graph using PAGA 1.2 algorithm, Wolf et al 2019, Genome Biolo...
Collapse Graph By Sum
Calculates factor-stratified sums for each column
Compute Chebyshev Coefficients
Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot for deta...
Set colors for embedding plot. Used primarily in embeddingPlot().
Plotting function for cluster labels, names contain cell names. Used p...
Plot embedding with provided labels / colors using ggplot2
Embed a graph into a UMAP, Uniform Manifold Approximation and Projecti...
Embed a k-nearest neighbor (kNN) graph within a UMAP. Used within embe...
Extend matrix to include new columns in matrix
Utility function to translate a factor into colors
Encodes logic of how to handle named-vector and functional palettes. U...
Get nearest neighbors method on graph
Collapse vertices belonging to each cluster in a graph
Convert igraph graph into an adjacency list
Graph filter with the heat kernel: $f(x) = exp(-\beta |x / \lambda_m -...
Jensen–Shannon distance metric (i.e. the square root of the Jensen–Sha...
Merge list of count matrices into a common matrix, entering 0s for the...
Translate multilevel segmentation into a dendrogram, with the lowest l...
Parallel, optionally verbose lapply. See ?parallel::mclapply for more ...
Label propagation
Estimate labeling distribution for each vertex, based on provided labe...
Estimate labeling distribution for each vertex, based on provided labe...
Propagate labels using Zhu, Ghahramani, Lafferty (2003) algorithm, "Se...
Save DE results as JSON tables for viewing in browser
Set range for values in object. Changes values outside of range to min...
Smooth gene expression, used primarily within conos::correctGenes. Use...
Smooth with Chebyshev Polynomials
Smooth Signal on Graph
Set names equal to values, a stats::setNames wrapper function
splitVectorByNodes
Set plot.theme, legend, ticks for embedding plot. Used primarily in em...
Utility function to translate values into colors.
Helper function to return a ggplot color gradient for a numeric vector...
Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.