Core Utilities for Single-Cell RNA-Seq

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.

Readme

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

Functions in sccore

Name	Description
conosGraph	Conos graph
dotPlot	Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot for details
extendMatrix	Extend matrix to include new columns in matrix
embeddingPlot	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
setMinMax	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
sn	Set names equal to values, a stats::setNames wrapper function
fac2col	Utility function to translate a factor into colors
colSumByFac	Calculates factor-stratified sums for each column
heatFilter	Graph filter with the heat kernel: $$f(x) = exp(-\beta \|x / \lambda_m - a\|^b)$$
graphToAdjList	Convert igraph graph into an adjacency list
jsDist	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
fac2palette	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().
umapEmbedding	UMAP embedding
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
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>
splitVectorByNodes	splitVectorByNodes
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.
multi2dend	Translate multilevel segmentation into a dendrogram, with the lowest level of the dendrogram listing the cells
val2ggcol	Helper function to return a ggplot color gradient for a numeric vector ggplot(aes(color=x, ...), ...) + val2ggcol(x)
val2col	Utility function to translate values into colors.
plapply	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>
as_factor	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
No Results!

Name

Description

conosGraph

Conos graph

dotPlot

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

extendMatrix

Extend matrix to include new columns in matrix

embeddingPlot

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

setMinMax

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

fac2col

Utility function to translate a factor into colors

colSumByFac

Calculates factor-stratified sums for each column

heatFilter

Graph filter with the heat kernel: $$f(x) = exp(-\beta |x / \lambda_m - a|^b)$$

graphToAdjList

Convert igraph graph into an adjacency list

jsDist

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

fac2palette

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().

umapEmbedding

UMAP embedding

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

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>

splitVectorByNodes

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.

multi2dend

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

val2ggcol

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

val2col

Utility function to translate values into colors.

plapply

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>

as_factor

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

No Results!

Details

License	GPL-3
Encoding	UTF-8
LazyData	true
RoxygenNote	7.1.1
LinkingTo	Rcpp, RcppArmadillo, RcppProgress, RcppEigen
NeedsCompilation	yes
SystemRequirements	C++11
URL	https://github.com/kharchenkolab/sccore
BugReports	https://github.com/kharchenkolab/sccore/issues
Packaged	2021-02-20 10:11:55 UTC; evanbiederstedt
Repository	CRAN
Date/Publication	2021-02-23 12:20:03 UTC

imports	dplyr , ggplot2 , ggrepel , graphics , grDevices , igraph , irlba , magrittr , Matrix , methods , parallel , pbmcapply , pROC , Rcpp , rlang , scales , tibble , utils , uwot , withr
suggests	ggrastr (>= 0.1.7) , rmumps , testthat
depends	R (>= 3.5.0)
linkingto	RcppArmadillo , RcppEigen , RcppProgress
Contributors	Peter Kharchenko, Viktor Petukhov, Ramus Rydbirk

sccore v0.1.2