sccore

List of adjacent vertices from igraph object

List of adjacent vertex weights from igraph object

Append specificity metrics to DE

convert character vector into a factor with names "values" and "levels"

Conos cell annotations

Calculates factor-stratified sums for each column

Collapse count matrices by cell type, given min/max number of cells

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>

Collapse Graph By Sum

Compute Chebyshev Coefficients

Conos clusters list

Conos graph

Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot for details

Embed a graph into a UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction, <https://github.com/lmcinnes/umap>, <doi:10.21105/joss.00861>

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.

Set colors for embedding plot. Used primarily in embeddingPlot().

Plotting function for cluster labels, names contain cell names. Used primarily in embeddingPlot().

Plot embedding with provided labels / colors using ggplot2

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. Used primarily within embeddingGroupPlot()

Collapse vertices belonging to each cluster in a graph

Get nearest neighbors method on graph

Convert igraph graph into an adjacency list

Graph filter with the heat kernel:

Jensen–Shannon distance metric (i.e. the square root of the Jensen–Shannon divergence) between the columns of a dense matrix m

Merge list of count matrices into a common matrix, entering 0s for the missing entries

Translate multilevel segmentation into a dendrogram, with the lowest level of the dendrogram listing the cells

Parallel, optionally verbose lapply. See ?parallel::mclapply for more info.

Estimate labeling distribution for each vertex, based on provided labels.

Estimate labeling distribution for each vertex, based on provided labels using a Random Walk on graph

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>

Label propagation

Set range for values in object. Changes values outside of range to min or max. Adapted from Seurat::MinMax

Smooth with Chebyshev Polynomials

Smooth Signal on Graph

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))

Set names equal to values, a stats::setNames wrapper function

splitVectorByNodes

Set plot.theme, legend, ticks for embedding plot. Used primarily in embeddingPlot().

UMAP embedding

Utility function to translate values into colors.

Helper function to return a ggplot color gradient for a numeric vector ggplot(aes(color=x, ...), ...) + val2ggcol(x)