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sccore

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, collapsing vertices of each cluster in the graph, and propagating graph labels.

Installation

To install the stable version from CRAN, use:

install.packages('sccore')

To install the latest version, use:

install.packages('devtools')
devtools::install_github('kharchenkolab/sccore')

Citation

If you find sccore useful for your publication, please cite:

Viktor Petukhov, Ramus Rydbirk, Peter Kharchenko and Evan Biederstedt
(2021). sccore: Core Utilities for Single-Cell RNA-Seq. R package
version 0.1.2. https://github.com/kharchenkolab/sccore

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Version

Install

install.packages('sccore')

Monthly Downloads

2,151

Version

0.1.2

License

GPL-3

Issues

Pull Requests

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Repository

https://github.com/kharchenkolab/sccore

Maintainer

Evan Biederstedt

Last Published

February 23rd, 2021

Functions in sccore (0.1.2)

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

propagateLabelsDiffusion

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

propagateLabels

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

embeddingGroupPlot

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

embeddingColorsPlot

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

getClusterGraph

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

Get nearest neighbors method on graph

smoothChebyshev

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

mergeCountMatrices

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()

styleEmbeddingPlot

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

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

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

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_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))

smoothSignalOnGraph

Smooth Signal on Graph

collapseGraphSum

Collapse Graph By Sum

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>

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

cellAnnotations

Conos cell annotations

adjacent_vertex_weights

List of adjacent vertex weights from igraph object

adjacentVertices

List of adjacent vertices from igraph object

appendSpecificityMetricsToDE

Append specificity metrics to DE

conosClusterList

Conos clusters list

computeChebyshevCoeffs

Compute Chebyshev Coefficients