Package 'AUCell'

Title: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
Description: AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.
Authors: Sara Aibar, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium.
Maintainer: Gert Hulselmans <[email protected]>
License: GPL-3
Version: 1.29.0
Built: 2024-10-30 03:34:25 UTC
Source: https://github.com/bioc/AUCell

Help Index

AUCell_assignCells

Description

Assigns whether the gene sets are considered "active" on each cell based on the given thresholds

Usage

AUCell_assignCells(cellsAUC, thresholds, nCores = 1)

Arguments

cellsAUC

AUC object returned by AUCell_calcAUC.
thresholds

Thresholds selected for each geneset (named vector).
nCores

Number of cores to use for computation.

Value

List with the following elements for each gene-set:

  • 'aucThr' threshold value, in the same format as AUCell_exploreThresholds()

  • 'assignment' List of cells that pass the selected AUC threshold

See Also

Previous step in the workflow: AUCell_calcAUC and optionally AUCell_exploreThresholds

See the package vignette for examples and more details: vignette("AUCell")

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.

############# Fake expression matrix #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
dim(exprMatrix)
##################################################

######### Previous steps in the workflow #########
# Step 1.
cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats=FALSE)

# Step 2.
# (Gene sets: random genes)
geneSets <- list(geneSet1=sample(rownames(exprMatrix), 10),
                 geneSet2=sample(rownames(exprMatrix), 5))
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5)
##################################################

############## Step 3: Assign cells ##############

# 1. Plot histograms and obtain some pre-computed thresholds
# (this example is only meant to show the interface/arguments of the function,
# see the vignette for meaningful examples)
set.seed(123)
par(mfrow=c(1,2)) # Plot is divided into one row and two columns
thresholds <- AUCell_exploreThresholds(cells_AUC, plotHist=TRUE)
thresholds$geneSet1$aucThr

# 2. Obtain cells over a given threshold:
names(which(getAUC(cells_AUC)["geneSet1",] > 0.19))

# Alternative 1: assign cells according to the 'automatic' threshold
cells_assignment <- AUCell_exploreThresholds(cells_AUC,
                                             plotHist=FALSE, assignCells=TRUE)
# Cells assigned:
getAssignments(cells_assignment)
# Threshold applied:
getThresholdSelected(cells_assignment)

# Alternative 2: choose a threshold manually and assign cells
newThresholds = getThresholdSelected(cells_assignment)
newThresholds['geneSet1'] = 0.8
newAssignments = AUCell_assignCells(cells_AUC, newThresholds)
getAssignments(newAssignments)

Build gene expression rankings for each cell

Description

Builds the "rankings" for each cell: expression-based ranking for all the genes in each cell.

The genes with same expression value are shuffled. Therefore, genes with expression '0' are randomly sorted at the end of the ranking.

These "rankings" can be seen as a new representation of the original dataset. Once they are calculated, they can be saved for future analyses.

Usage

AUCell_buildRankings(
  exprMat,
  featureType = "genes",
  plotStats = TRUE,
  splitByBlocks = FALSE,
  BPPARAM = NULL,
  keepZeroesAsNA = FALSE,
  verbose = TRUE,
  nCores = NULL,
  mctype = NULL,
  ...
)

## S4 method for signature 'dgCMatrix'
AUCell_buildRankings(
  exprMat,
  featureType = "genes",
  plotStats = TRUE,
  splitByBlocks = TRUE,
  BPPARAM = NULL,
  keepZeroesAsNA = FALSE,
  verbose = TRUE,
  nCores = NULL,
  mctype = NULL
)

## S4 method for signature 'matrix'
AUCell_buildRankings(
  exprMat,
  featureType = "genes",
  plotStats = TRUE,
  splitByBlocks = FALSE,
  BPPARAM = NULL,
  keepZeroesAsNA = FALSE,
  verbose = TRUE,
  nCores = NULL,
  mctype = NULL
)

## S4 method for signature 'ExpressionSet'
AUCell_buildRankings(
  exprMat,
  featureType = "genes",
  plotStats = TRUE,
  splitByBlocks = FALSE,
  BPPARAM = NULL,
  keepZeroesAsNA = FALSE,
  verbose = TRUE,
  nCores = NULL,
  mctype = NULL
)

## S4 method for signature 'SummarizedExperiment'
AUCell_buildRankings(
  exprMat,
  featureType = "genes",
  plotStats = TRUE,
  splitByBlocks = FALSE,
  BPPARAM = NULL,
  keepZeroesAsNA = FALSE,
  verbose = TRUE,
  assayName = NULL,
  nCores = NULL,
  mctype = NULL
)

Arguments

exprMat

Expression matrix (genes as rows, cells as columns) The expression matrix can also be provided as one of the R/Bioconductor classes:

  • dgCMatrix-class: Sparse matrix

  • RangedSummarizedExperiment and derived classes (e.g. SingleCellExperiment ): The matrix will be obtained through assay(exprMatrix), -which will extract the first assay (usually the counts)- or the assay name given in 'assayName'

  • ExpressionSet: The matrix will be obtained through exprs(exprMatrix)

featureType

Name for the rows (e.g. "genes"). Only for naming the rankings, not used internally.
plotStats

Should the function plot the expression boxplots/histograms? (TRUE / FALSE). These plots can also be produced with the function plotGeneCount.
splitByBlocks

Whether to split the matrix by blocks in the ranking calculation. Allows using multiple cores. FALSE by default. If using sparse matrices it is automatically set to TRUE.
BPPARAM

Set to use multiple cores. Only used if 'splitByBlocks=TRUE'
keepZeroesAsNA

Convert zeroes to NA instead of locating randomly at the end of the ranking.
verbose

Should the function show progress messages? (TRUE / FALSE)
nCores

Deprecated
mctype

Deprecated
...

Other arguments
assayName

Name of the assay containing the expression matrix (e.g. in SingleCellExperiment objects)

Details

It is important to check that most cells have at least the number of expressed/detected genes that are going to be used to calculate the AUC ('aucMaxRank' in 'calcAUC()'). The histogram provided by 'AUCell_buildRankings()' allows to quickly check this distribution. 'plotGeneCount(exprMatrix)' allows to obtain only the plot before building the rankings.

Value

Ranking of the feature within the cell (features as rows, cells as columns)

See Also

Next step in the workflow: AUCell_calcAUC.

See the package vignette for examples and more details: vignette("AUCell")

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.

############# Fake expression matrix #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
##################################################

cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats=TRUE)
cells_rankings

Calculate AUC

Description

Calculates the 'AUC' for each gene-set in each cell.

Usage

AUCell_calcAUC(
  geneSets,
  rankings,
  nCores = 1,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(rankings)),
  verbose = TRUE
)

## S4 method for signature 'list'
AUCell_calcAUC(
  geneSets,
  rankings,
  nCores = 1,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(rankings)),
  verbose = TRUE
)

## S4 method for signature 'character'
AUCell_calcAUC(
  geneSets,
  rankings,
  nCores = 1,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(rankings)),
  verbose = TRUE
)

## S4 method for signature 'GeneSet'
AUCell_calcAUC(
  geneSets,
  rankings,
  nCores = 1,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(rankings)),
  verbose = TRUE
)

## S4 method for signature 'GeneSetCollection'
AUCell_calcAUC(
  geneSets,
  rankings,
  nCores = 1,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(rankings)),
  verbose = TRUE
)

Arguments

geneSets

List of gene-sets (or signatures) to test in the cells. The gene-sets should be provided as GeneSet, GeneSetCollection or character list (see examples).
rankings

'Rankings' created for this dataset with AUCell_buildRankings.
nCores

Number of cores to use for computation.
normAUC

Wether to normalize the maximum possible AUC to 1 (Default: TRUE).
aucMaxRank

Threshold to calculate the AUC (see 'details' section)
verbose

Should the function show progress messages? (TRUE / FALSE)

Details

In a simplified way, the AUC value represents the fraction of genes, within the top X genes in the ranking, that are included in the signature. The parameter 'aucMaxRank' allows to modify the number of genes (maximum ranking) that is used to perform this computation. By default, it is set to 5% of the total number of genes in the rankings. Common values may range from 1 to 20%.

Value

Matrix with the AUC values (gene-sets as rows, cells as columns).

See Also

Previous step in the workflow: AUCell_buildRankings. Next step in the workflow: AUCell_exploreThresholds.

See the package vignette for examples and more details: vignette("AUCell")

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.

############# Fake expression matrix #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
##################################################

######### Previous step in the workflow ##########
# Step 1.
cells_rankings <- AUCell_buildRankings(exprMatrix)
##################################################

############## Step 2: Calculate AUC #############

# In this example we use two gene sets: 10 and 5 random genes
# (see other formatting examples at the end)
fewGenes <- sample(rownames(exprMatrix), 10)
otherGenes <- sample(rownames(exprMatrix), 5)

geneSets <- list(geneSet1=fewGenes,
                 geneSet2=otherGenes)
geneSets

# Calculate AUC with the rankings from Step 1.
# To be able to run this fake example (which contain only 20 genes),
# we use aucMaxRank=5 (top 25% of the genes in the ranking)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1)

# Format of the output:
cells_AUC

# To subset & access the AUC slot (as matrix):
cells_AUC[1:2,]
cells_AUC[,3:4]
getAUC(cells_AUC)[,1:5]


# These methods are also available:
dim(cells_AUC)
nrow(cells_AUC)
ncol(cells_AUC)
colnames(cells_AUC)[1:4]
rownames(cells_AUC)

#########################################################
# Alternatives for the input of gene sets:

# a) Character vector (i.e. only one gene-set)
# It will take the default name 'geneSet'
fewGenes
test <- AUCell_calcAUC(fewGenes, cells_rankings, aucMaxRank=5)

# b) List
geneSets <- list(geneSet1=fewGenes,
                 geneSet2=otherGenes)
geneSets
test <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5)

# c) GeneSet object (from GSEABase)
library(GSEABase)
geneSetOne <- GeneSet(fewGenes, setName="geneSetOne")
geneSetOne
test <- AUCell_calcAUC(geneSetOne, cells_rankings, aucMaxRank=5)


# d) GeneSetCollection object (from GSEABase)
geneSetTwo <- GeneSet(otherGenes, setName="geneSetTwo")
geneSets <- GeneSetCollection(geneSetOne, geneSetTwo)
geneSets
test <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5)

AUCell_exploreThresholds

Description

Plots all the AUC histograms (per gene-set) and calculates several likely thresholds for each gene-set

Usage

AUCell_exploreThresholds(
  cellsAUC,
  thrP = 0.01,
  nCores = 1,
  smallestPopPercent = 0.25,
  plotHist = TRUE,
  densAdjust = 2,
  assignCells = FALSE,
  nBreaks = 100,
  verbose = TRUE
)

getThresholdSelected(aucellThresholds)

getAssignments(aucellThresholds)

Arguments

cellsAUC

AUC object returned by AUCell_calcAUC.
thrP

Probability to determine outliers in some of the distributions (see 'details' section).

By default it is set to 1% (thrP): if there are 3000 cells in the dataset, it is expected that approximately 30 cells are over this threshold if the AUC is normally distributed.
nCores

Number of cores to use for computation.
smallestPopPercent

Size (percentage) of the smallest population of cells expected. Used to calculate some of the thresholds.
plotHist

Whether to plot the AUC histograms. (TRUE / FALSE)
densAdjust

Parameter for the density curve. (See density for details).
assignCells

Return the list of cells that pass the automatically selected threshold? (TRUE/FALSE)
nBreaks

Number of bars to plot in the histograms.
verbose

Should the function show progress messages? (TRUE / FALSE)
aucellThresholds

For aux functions: Output from AUCell_exploreThresholds

Details

To ease the selection of an assignment theshold, this function adjusts the AUCs of each gene-set to several distributions and calculates possible thresholds:

  • minimumDens (plot in Blue): Inflection point of the density curve. This is usually a good option for the ideal situation with bimodal distributions.

    To avoid false positives, by default this threshold will not be chosen if the second distribution is higher (i.e. the majority of cells have the gene-set "active").

  • L_k2 (plot in Red): Left distribution, after adjusting the AUC to a mixture of two distributions. The threshold is set to the right (prob: 1-(thrP/nCells)). Only available if 'mixtools' package is installed.

  • R_k3 (plot in Pink): Right distribution, after adjusting the AUC to a mixture of three distributions. The threshold is set to the left (prob: thrP). Only available if 'mixtools' package is installed.

  • Global_k1 (plot in Grey): "global" distribution (i.e. mean and standard deviations of all cells). The threshold is set to the right (prob: 1-(thrP/nCells)).

    The threshold based on the global distribution is ignored from the automatic selection unless the mixed models are overlapping.

Note: If assignCells=TRUE, the highest threshold is used to select cells. However, keep in mind that this function is only meant to ease the selection of the threshold, and we highly recommend to look at the AUC histograms and adjust the threshold manually if needed. We recommend to be specially aware on gene-sets with few genes (10-15) and thresholds that are set extremely low.

Value

List with the following elements for each gene-set:

  • 'aucThr' Thresholds calculated with each method (see 'details' section), and the number of cells that would be assigned using that threshold.

    If assignCells=TRUE, the threshold selected automatically is the highest value (in most cases, excluding the global distribution).

  • 'assignment' List of cells that pass the selected AUC threshold (if assignCells=TRUE)

If plotHist=TRUE the AUC histogram is also plot, including the distributions calculated and the corresponding thresholds in the same color (dashed vertical lines). The threshold that is automatically selected is shown as a thicker non-dashed vertical line.

See Also

Previous step in the workflow: AUCell_calcAUC.

See the package vignette for examples and more details: vignette("AUCell")

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.

############# Fake expression matrix #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
dim(exprMatrix)
##################################################

######### Previous steps in the workflow #########
# Step 1.
cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats=FALSE)

# Step 2.
# (Gene sets: random genes)
geneSets <- list(geneSet1=sample(rownames(exprMatrix), 10),
                 geneSet2=sample(rownames(exprMatrix), 5))
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5)
##################################################

############## Step 3: Assign cells ##############

# 1. Plot histograms and obtain some pre-computed thresholds
# (this example is only meant to show the interface/arguments of the function,
# see the vignette for meaningful examples)
set.seed(123)
par(mfrow=c(1,2)) # Plot is divided into one row and two columns
thresholds <- AUCell_exploreThresholds(cells_AUC, plotHist=TRUE)
thresholds$geneSet1$aucThr

# 2. Obtain cells over a given threshold:
names(which(getAUC(cells_AUC)["geneSet1",] > 0.19))

# Alternative 1: assign cells according to the 'automatic' threshold
cells_assignment <- AUCell_exploreThresholds(cells_AUC,
                                             plotHist=FALSE, assignCells=TRUE)
# Cells assigned:
getAssignments(cells_assignment)
# Threshold applied:
getThresholdSelected(cells_assignment)

# Alternative 2: choose a threshold manually and assign cells
newThresholds = getThresholdSelected(cells_assignment)
newThresholds['geneSet1'] = 0.8
newAssignments = AUCell_assignCells(cells_AUC, newThresholds)
getAssignments(newAssignments)

Plot AUC histogram

Description

Plots the distribution of AUC across the cells (for each gene-set) as an histogram.

Usage

AUCell_plotHist(
  cellsAUC,
  aucThr = max(cellsAUC),
  nBreaks = 100,
  onColor = "dodgerblue4",
  offColor = "slategray2",
  ...
)

Arguments

cellsAUC

Subset of the object returned by AUCell_calcAUC (i.e. including only the gene-sets to plot)
aucThr

AUC value planned to use as threshold (to make sure the X axis includes it), if any. Otherwise, the X axis extends to cover only the AUC values plotted.
nBreaks

Number of 'bars' to plot (breaks argument for hist function).
onColor

Color for the bars that pass the AUC threshold
offColor

Color for the bars that do not pass the AUC threshold
...

Other arguments to pass to hist function.

Value

List of histogram objects (invisible).

See Also

See the package vignette for examples and more details: vignette("AUCell")

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.

############# Fake expression matrix #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
dim(exprMatrix)
##################################################

############# Begining of the workflow ###########
# Step 1.
cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats=FALSE)

# Step 2.
# (Gene set: 10 random genes)
genes <- sample(rownames(exprMatrix), 10)
geneSets <- list(geneSet1=genes)
# (aucMaxRank=5 to run with this fake example, it will return 'high' AUC values)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5)
##################################################

# Plot histogram:
AUCell_plotHist(cells_AUC["geneSet1",], nBreaks=10)

Plot

Description

Plots the AUC histogram and t-SNE coloured by AUC, binary activity and TF expression

Usage

AUCell_plotTSNE(
  tSNE,
  exprMat = NULL,
  cellsAUC = NULL,
  thresholds = NULL,
  reorderGeneSets = FALSE,
  cex = 1,
  alphaOn = 1,
  alphaOff = 0.2,
  borderColor = adjustcolor("lightgray", alpha.f = 0.1),
  offColor = "lightgray",
  plots = c("histogram", "binaryAUC", "AUC", "expression"),
  exprCols = c("goldenrod1", "darkorange", "brown"),
  asPNG = FALSE,
  ...
)

Arguments

tSNE

t-SNE coordinates (e.g. tSNE$Y)
exprMat

Expression matrix
cellsAUC

AUC (as returned by calcAUC)
thresholds

Thresholds returned by AUCell
reorderGeneSets

Whether to reorder the gene sets based on AUC similarity
cex

Scaling factor for the dots in the scatterplot
alphaOn

Transparency for the dots representing "active" cells
alphaOff

Transparency for the dots representing "inactive" cells
borderColor

Border color for the dots (scatterplot)
offColor

Color for the dots representing "inactive" cells
plots

Which plots to generate? Select one or multiple: plots=c("histogram", "binaryAUC", "AUC", "expression")
exprCols

Color scale for the expression
asPNG

Output each individual plot in a .png file? (can also be a directory)
...

Other arguments to pass to hist function.

Details

To avoid calculating thresholds, set thresholds to FALSE

Value

Returns invisible: cells_trhAssignment

See Also

List of vignettes included in the package: vignette(package="AUCell")

Examples

######
# Fake run of AUCell
set.seed(123)
exprMatrix <- matrix(
  data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
  nrow=20, 
  dimnames=list(paste("Gene", 1:20, sep=""), 
                paste("Cell", 1:500, sep="")))
geneSets <- list(geneSet1=sample(rownames(exprMatrix), 10),
                 geneSet2=sample(rownames(exprMatrix), 5))

cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats = FALSE)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1)
selectedThresholds <- rowMeans(getAUC(cells_AUC))
cellsTsne<- Rtsne::Rtsne(t(exprMatrix),max_iter = 10)$Y
# cellsTsne<- tsne::tsne(t(exprMatrix),max_iter = 10)
rownames(cellsTsne) <- colnames(exprMatrix)
######


par(mfrow=c(2,3))
thrs <- AUCell_plotTSNE(tSNE=cellsTsne, exprMat=NULL,
                        cellsAUC=cells_AUC, thresholds=selectedThresholds, 
                        plots = c("histogram", "binaryAUC", "AUC"))
 


#####
# Color based on the known phenodata:
cellInfo <- data.frame(cellType1=sample(LETTERS[1:3],ncol(exprMatrix), replace=TRUE), 
                       cellType2=sample(letters[5:7],ncol(exprMatrix), replace=TRUE), 
                       nGenes=abs(rnorm(ncol(exprMatrix))), 
                       row.names=colnames(exprMatrix))
colVars <- list(cellType2=setNames(c("skyblue","magenta", "darkorange"),letters[5:7]))
# dev.off()
plotTsne_cellProps(cellsTsne, cellInfo, colVars=colVars)

Run AUCell

Description

Runs AUCell (calculates the ranking + score genesets)

Usage

AUCell_run(
  exprMat,
  geneSets,
  featureType = "genes",
  keepZeroesAsNA = FALSE,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(exprMat)),
  BPPARAM = NULL,
  ...
)

## S4 method for signature 'dgCMatrix'
AUCell_run(
  exprMat,
  geneSets,
  featureType = "genes",
  keepZeroesAsNA = FALSE,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(exprMat)),
  BPPARAM = NULL
)

## S4 method for signature 'matrix'
AUCell_run(
  exprMat,
  geneSets,
  featureType = "genes",
  keepZeroesAsNA = FALSE,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(exprMat)),
  BPPARAM = NULL
)

## S4 method for signature 'SummarizedExperiment'
AUCell_run(
  exprMat,
  geneSets,
  featureType = "genes",
  keepZeroesAsNA = FALSE,
  normAUC = TRUE,
  aucMaxRank = ceiling(0.05 * nrow(exprMat)),
  BPPARAM = NULL,
  assayName = NULL
)

Arguments

exprMat

Expression matrix (genes/regions as rows, cells as columns) The expression matrix can also be provided as one of the R/Bioconductor classes:

geneSets

List of gene-sets (or signatures) to test in the cells. The gene-sets should be provided as GeneSet, GeneSetCollection or character list (see examples).
featureType

Name for the rows (e.g. "genes"). Only for naming the rankings, not used internally.
keepZeroesAsNA

Convert zeroes to NA instead of locating randomly at the end of the ranking.
normAUC

Whether to normalize the maximum possible AUC to 1 (Default: TRUE).
aucMaxRank

Threshold to calculate the AUC (see 'details' section)
BPPARAM

Set to use multiple cores. Only used if 'splitByBlocks=TRUE'
...

Other arguments
assayName

Name of the assay containing the expression matrix (e.g. in SingleCellExperiment objects)

Details

In a simplified way, the AUC value represents the fraction of genes, within the top X genes in the ranking, that are included in the signature. The parameter 'aucMaxRank' allows to modify the number of genes (maximum ranking) that is used to perform this computation. By default, it is set to 5% of the total number of genes in the rankings. Common values may range from 1 to 20%.

Value

Matrix with the AUC values (gene-sets as rows, cells as columns).

See Also

Includes AUCell_buildRankings and AUCell_calcAUC. Next step in the workflow: AUCell_exploreThresholds.

See the package vignette for examples and more details: vignette("AUCell")

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.

############# Fake expression matrix #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
exprMatrix <- as(exprMatrix, "dgCMatrix")

# In this example we use two gene sets: 10 and 5 random genes
# (see other formatting examples at the end)
fewGenes <- sample(rownames(exprMatrix), 10)
otherGenes <- sample(rownames(exprMatrix), 5)

geneSets <- list(geneSet1=fewGenes,
                 geneSet2=otherGenes)
geneSets

# Calculate AUCell score for the genes in the sets
# To be able to run this fake example (which contain only 20 genes),
# we use aucMaxRank=5 (top 25% of the genes in the ranking)
cells_AUC <- AUCell_run(exprMatrix, geneSets, aucMaxRank=5)


## To run in paralell:
# cells_AUC <- AUCell_run(exprMatrix, geneSets, aucMaxRank=5, 
#                   BPPARAM=BiocParallel::MulticoreParam(5))



# Format of the output:
cells_AUC

# To subset & access the AUC slot (as matrix):
cells_AUC[1:2,]
cells_AUC[,3:4]
getAUC(cells_AUC)[,1:5]


# These methods are also available:
dim(cells_AUC)
nrow(cells_AUC)
ncol(cells_AUC)
colnames(cells_AUC)[1:4]
rownames(cells_AUC)

#########################################################
# Alternatives for the input of gene sets:

# a) Character vector (i.e. only one gene-set)
# It will take the default name 'geneSet'
fewGenes
test <- AUCell_run(exprMatrix, fewGenes, aucMaxRank=5)

# b) List
geneSets <- list(geneSet1=fewGenes,
                 geneSet2=otherGenes)
geneSets
test <- AUCell_run(exprMatrix, fewGenes, aucMaxRank=5)

# c) GeneSet object (from GSEABase)
library(GSEABase)
geneSetOne <- GeneSet(fewGenes, setName="geneSetOne")
geneSetOne
test <- AUCell_run(exprMatrix, fewGenes, aucMaxRank=5)


# d) GeneSetCollection object (from GSEABase)
geneSetTwo <- GeneSet(otherGenes, setName="geneSetTwo")
geneSets <- GeneSetCollection(geneSetOne, geneSetTwo)
geneSets
test <- AUCell_run(exprMatrix, fewGenes, aucMaxRank=5)

Wrapper to the matrix that stores the AUC or the cell rankings.

Description

This class extends SummarizedExperiment to contain the AUC matrix and cell rankings (as 'assays').

The results are stored in the assays slot, but they can be accessed through the regular methods (i.e. nrow, rownames... )

Types:

- "AUC": The assays contains the AUC for the gene-sets (or region-sets) & cells.

- "ranking": The assays contains the gene rankings for each cell.

Usage

## S4 method for signature 'aucellResults'
show(object)

getAUC(object)

## S4 method for signature 'aucellResults'
getAUC(object)

getRanking(object)

## S4 method for signature 'aucellResults'
getRanking(object)

## S4 method for signature 'aucellResults'
cbind(..., deparse.level = 1)

## S4 method for signature 'aucellResults'
rbind(..., deparse.level = 1)

Arguments

object

Results from AUCell_buildRanking
...

(Only for cbind)

or AUCell_calcAUC.
deparse.level

(Only for cbind)

Value

  • show: Prints a summary of the object

  • getAUC: Returns the matrix containing the AUC

  • getRanking: Returns the matrix containing the rankings

  • cbind: Combines objects by columns (cbind on assays); other other slots are conserved from the first object provided as argument. Both, ranking and AUC are calculated by column (cell or sample). Therefore, it is fine to merge objects as long as they come from equivalent datasets (and keep same genes/genesets, etc...)

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.


############# Fake run of AUCell #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
dim(exprMatrix)

# Running AUCell
cells_rankings <- AUCell_buildRankings(exprMatrix)
fewGenes <- sample(rownames(exprMatrix), 10)
otherGenes <- sample(rownames(exprMatrix), 5)
geneSets <- list(geneSet1=fewGenes,
                 geneSet2=otherGenes)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1)
##############################################

#Exploring the output:
cells_AUC

class(cells_AUC)

# Extracting the AUC matrix:
getAUC(cells_AUC)[,1:5]

# Subsetting and regular manipulation methods are also available:
cells_AUC[1:2,]
cells_AUC[,3:4]

dim(cells_AUC)
nrow(cells_AUC)
ncol(cells_AUC)
colnames(cells_AUC)
rownames(cells_AUC)

### Merging 2 objects (ranking or AUC):
sample1 <- cells_AUC[,10:20]
sample2 <- cells_AUC[,100:140]
cbind(sample1, sample2)

Get gene set name (excluding number of genes/regions after space)

Description

Returns the gene set name (i.e. selects the given pattern)

Usage

getSetNames(aucMat, patterns, startChr = "^", endChr = " |_")

Arguments

aucMat

AUC matrix
patterns

patterns
startChr

Character to indicate the start (typically "^")
endChr

Character at the end of the gene set name, i.e. space or "_" after a transcription factor name

Value

Returns the gene set name (i.e. selects the given pattern)

GeneSet methods

Description

Functions to manipulate GeneSet and GeneSetCollection objects (from package GSEABase)

Usage

nGenes(geneSet)

## S4 method for signature 'GeneSet'
nGenes(geneSet)

## S4 method for signature 'GeneSetCollection'
nGenes(geneSet)

subsetGeneSets(geneSets, geneNames)

## S4 method for signature 'GeneSetCollection'
subsetGeneSets(geneSets, geneNames)

setGeneSetNames(geneSets, newNames)

## S4 method for signature 'GeneSetCollection'
setGeneSetNames(geneSets, newNames)

Arguments

geneSet

One gene-set (GeneSet)
geneSets

Gene-set collection (GeneSetCollection)
geneNames

Gene names (for subset)
newNames

New names (to assign to the gene sets)

Value

- **nGenes()**: provides the number of genes in the gene-set, or each of the gene-sets in a collection

- **subsetGeneSets()**: Subsets each of the gene-sets in a collection to contain only the genes inthe given list. Equivalent to intersect(), but keeping the original gene-set name.

- **setGeneSetNames()**: Modifies the name of each gene-set in a collection

Examples

library(GSEABase)
genes_1 <- GeneSet(paste("Gene", 1:20, sep=""), setName="geneSet1")
genes_2 <- GeneSet(paste("Gene", 18:22, sep=""), setName="geneSet2")
geneSets <- GeneSetCollection(genes_1, genes_2)

nGenes(genes_1)
nGenes(geneSets)

subsetGeneSets(geneSets, paste("Gene", 15:20, sep=""))

geneSets_newNames <- setGeneSetNames(geneSets, c("one", "two"))
names(geneSets_newNames)

orderAUC

Description

Reorder the gene-sets based on AUC similarity

Usage

orderAUC(auc)

Arguments

auc

AUC (as returned by calcAUC)

Value

gene-set names in the suggested order

Examples

# cellsAUC <- cellsAUC[orderAUC(cellsAUC),]

plotEmb_rgb

Description

Colors the embeddings (t-SNE/Umap) based on the activity of 3 (groups of) geneSets

Usage

plotEmb_rgb(
  aucMat,
  embedding,
  geneSetsByCol,
  aucType = "AUC",
  aucMaxContrast = 0.8,
  offColor = "#c0c0c030",
  showPlot = TRUE,
  showLegend = TRUE,
  ...
)

Arguments

aucMat

AUC matrix (continuous or binary)
embedding

AUC matrix (continuous or binary)
geneSetsByCol

Gene sets to plot
aucType

"AUC" or "Binary"
aucMaxContrast

To increase the AUC contrast decrease the value.
offColor

Color por the cells completelly off. To deactivate (color as black), set to NULL.
showPlot

Whether to plot the coloured embeddings.
showLegend

Whether to plot add a legend to the plot.
...

Other arguments to pass to the plot function.

Value

The cell colors (invisible)

plotGeneCount

Description

Plots a histogram and boxplot for the number of genes detected in each cell.

Usage

plotGeneCount(exprMat, plotStats = TRUE, verbose = TRUE)

Arguments

exprMat

Expression matrix (genes as rows, cells as columns)
plotStats

Logical. If true, it plots the histogram, otherwise only calculates the percentages of genes detected.
verbose

Should the function show progress messages? (TRUE / FALSE)

Details

It is important to check that most cells have at least the number of expressed/detected genes that are going to be used to calculate the AUC ('aucMaxRank' in 'calcAUC()'). The histogram provided by 'AUCell_buildRankings()' allows to quickly check this distribution. 'plotGeneCount(exprMatrix)' allows to obtain only the plot before building the rankings.

Value

Quantiles with the number of genes detected by cell (invisible). his result is also printed if verbose=TRUE.

See Also

See the package vignette for more details: vignette("AUCell")

Examples

### (Fake expression matrix)
exprMatrix <- matrix(sample(c(rep(0, 500), sample(1:3, 500, replace=TRUE))),
 nrow=20)
rownames(exprMatrix) <- paste("Gene", 1:20, sep="")
colnames(exprMatrix) <- paste("Sample", 1:50, sep="")
###

plotGeneCount(exprMatrix)
title(sub="Fake expression matrix")

plotTsne_cellProps

Description

Plots the t-SNE coloured based on the known the cell properties

Usage

plotTsne_cellProps(
  tSNE,
  cellInfo,
  colVars = NULL,
  cex = 1,
  sub = "",
  gradientCols = c("yellow", "orange", "red"),
  showLegend = TRUE
)

Arguments

tSNE

t-SNE coordinates (e.g. tSNE$Y)
cellInfo

Dataframe with cell phenodata
colVars

Colors for the cell properties (optional)
cex

Scaling factor for the dots in the scatterplot
sub

Subtitle (e.g. tSNE type)
gradientCols

Gradient colors for numerical variables
showLegend

Whether to show the legend

Value

Plots the t-SNE

Examples

######
# Fake run of AUCell
set.seed(123)
exprMatrix <- matrix(
  data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
  nrow=20, 
  dimnames=list(paste("Gene", 1:20, sep=""), 
                paste("Cell", 1:500, sep="")))
geneSets <- list(geneSet1=sample(rownames(exprMatrix), 10),
                 geneSet2=sample(rownames(exprMatrix), 5))

cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats = FALSE)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1)
selectedThresholds <- rowMeans(getAUC(cells_AUC))
cellsTsne<- Rtsne::Rtsne(t(exprMatrix),max_iter = 10)$Y
# cellsTsne<- tsne::tsne(t(exprMatrix),max_iter = 10)
rownames(cellsTsne) <- colnames(exprMatrix)
######


par(mfrow=c(2,3))
thrs <- AUCell_plotTSNE(tSNE=cellsTsne, exprMat=NULL,
                        cellsAUC=cells_AUC, thresholds=selectedThresholds, 
                        plots = c("histogram", "binaryAUC", "AUC"))
 


#####
# Color based on the known phenodata:
cellInfo <- data.frame(cellType1=sample(LETTERS[1:3],ncol(exprMatrix), replace=TRUE), 
                       cellType2=sample(letters[5:7],ncol(exprMatrix), replace=TRUE), 
                       nGenes=abs(rnorm(ncol(exprMatrix))), 
                       row.names=colnames(exprMatrix))
colVars <- list(cellType2=setNames(c("skyblue","magenta", "darkorange"),letters[5:7]))
# dev.off()
plotTsne_cellProps(cellsTsne, cellInfo, colVars=colVars)

Update AUCell results

Description

Updates the AUC scores provided by AUCell from a previous version.

Usage

updateAucellResults(oldAucObject, objectType = "AUC")

Arguments

oldAucObject

Object to update
objectType

Either "AUC" or "ranking" indicating the object type

Value

Updated version of the object as aucellResults.

Examples

oldAuc <- matrix(data=1:2000, nrow=50, ncol=40)
updateAucellResults(oldAuc)