Conos graph
Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot for details
Extend matrix to include new columns in matrix
Plot embedding with provided labels / colors using ggplot2
Estimate labeling distribution for each vertex, based on provided labels using a Random Walk on graph
Estimate labeling distribution for each vertex, based on provided labels.
Plotting function for cluster labels, names contain cell names. Used primarily in embeddingPlot().
Set colors for embedding plot. Used primarily in embeddingPlot().
Collapse vertices belonging to each cluster in a graph
Set range for values in object. Changes values outside of range to min or max. Adapted from Seurat::MinMax
Get nearest neighbors method on graph
Smooth with Chebyshev Polynomials
Set names equal to values, a stats::setNames wrapper function
Utility function to translate a factor into colors
Calculates factor-stratified sums for each column
Graph filter with the heat kernel: $$f(x) = exp(-\beta |x / \lambda_m - a|^b)$$
Convert igraph graph into an adjacency list
Jensen<U+2013>Shannon distance metric (i.e. the square root of the Jensen<U+2013>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
Encodes logic of how to handle named-vector and functional palettes. Used primarily within embeddingGroupPlot()
Set plot.theme, legend, ticks for embedding plot. Used primarily in embeddingPlot().
UMAP embedding
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
Embed a graph into a UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction, <https://github.com/lmcinnes/umap>, <doi:10.21105/joss.00861>
splitVectorByNodes
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.
Translate multilevel segmentation into a dendrogram, with the lowest level of the dendrogram listing the cells
Helper function to return a ggplot color gradient for a numeric vector
ggplot(aes(color=x, ...), ...) + val2ggcol(x)
Utility function to translate values into colors.
Parallel, optionally verbose lapply. See ?parallel::mclapply for more info.
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))
Smooth Signal on Graph
Collapse Graph By Sum
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>
convert character vector into a factor with names "values" and "levels"
Conos cell annotations
List of adjacent vertex weights from igraph object
List of adjacent vertices from igraph object
appendSpecificityMetricsToDE
Append specificity metrics to DE
Conos clusters list
Compute Chebyshev Coefficients