Nothing
R/recursiveSplit.R
In celda: CEllular Latent Dirichlet Allocation
Defines functions
.createSCERecursiveSplitModule
.createSCERecursiveSplitCell
.recursiveSplitModule
.recursiveSplitModuleWithSeed
.recursiveSplitCell
.recursiveSplitCellWithSeed
.singleSplitY
.singleSplitZ
.singleSplitZ <- function(counts,
z,
s,
K,
minCell = 3,
alpha = 1,
beta = 1) {
zTa <- tabulate(z, K)
zToSplit <- which(zTa > minCell)
bestZ <- z
bestLl <- -Inf
for (i in zToSplit) {
clustLabel <- .celda_C(
counts[, z == i, drop = FALSE],
K = 2,
zInitialize = "random",
splitOnIter = -1,
splitOnLast = FALSE,
verbose = FALSE
)
if (length(unique(celdaClusters(clustLabel)$z)) == 2) {
ix <- z == i
newZ <- z
newZ[ix] <- ifelse(celdaClusters(clustLabel)$z == 2, i, K)
ll <- .logLikelihoodcelda_C(counts, s, newZ, K, alpha, beta)
if (ll > bestLl) {
bestZ <- newZ
bestLl <- ll
}
}
}
return(list(ll = bestLl, z = bestZ))
}
.singleSplitY <- function(counts,
y,
L,
minFeature = 3,
beta = 1,
delta = 1,
gamma = 1) {
yTa <- tabulate(y, L)
yToSplit <- which(yTa > minFeature)
bestY <- y
bestLl <- -Inf
# previousY <- y
for (i in yToSplit) {
clustLabel <- .celda_G(counts[y == i, , drop = FALSE],
L = 2,
yInitialize = "random",
splitOnIter = -1,
splitOnLast = FALSE,
nchains = 1,
verbose = FALSE
)
if (length(unique(celdaClusters(clustLabel)$y)) == 2) {
ix <- y == i
newY <- y
newY[ix] <- ifelse(celdaClusters(clustLabel)$y == 2, i, L)
ll <- .logLikelihoodcelda_G(counts, newY, L, beta, delta, gamma)
if (ll > bestLl) {
bestY <- newY
bestLl <- ll
}
}
}
return(list(ll = bestLl, y = bestY))
}
#' @title Recursive cell splitting
#' @description Uses the \link{celda_C} model to cluster cells into
#' population for range of possible K's. The cell population labels of the
#' previous "K-1" model are used as the initial values in the current model
#' with K cell populations. The best split of an existing cell population is
#' found to create the K-th cluster. This procedure is much faster than
#' randomly initializing each model with a different K. If module labels for
#' each feature are given in 'yInit', the \link{celda_CG} model will be used to
#' split cell populations based on those modules instead of individual
#' features. Module labels will also be updated during sampling and thus
#' may end up slightly different than \code{yInit}.
#' @param x A numeric \link{matrix} of counts or a
#' \linkS4class{SingleCellExperiment}
#' with the matrix located in the assay slot under \code{useAssay}.
#' Rows represent features and columns represent cells.
#' @param useAssay A string specifying the name of the
#' \link{assay}
#' slot to use. Default "counts".
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell
#' (column) in the count matrix.
#' @param initialK Integer. Minimum number of cell populations to try.
#' @param maxK Integer. Maximum number of cell populations to try.
#' @param tempL Integer. Number of temporary modules to identify and use in cell
#' splitting. Only used if \code{yInit = NULL}. Collapsing features to a
#' relatively smaller number of modules will increase the speed of clustering
#' and tend to produce better cell populations. This number should be larger
#' than the number of true modules expected in the dataset. Default NULL.
#' @param yInit Integer vector. Module labels for features. Cells will be
#' clustered using the \link{celda_CG} model based on the modules specified in
#' \code{yInit} rather than the counts of individual features. While the
#' features will be initialized to the module labels in \code{yInit}, the
#' labels will be allowed to move within each new model with a different K.
#' @param alpha Numeric. Concentration parameter for Theta. Adds a pseudocount
#' to each cell population in each sample. Default 1.
#' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount to
#' each feature in each cell (if \code{yInit} is NULL) or to each module in
#' each cell population (if \code{yInit} is set). Default 1.
#' @param delta Numeric. Concentration parameter for Psi. Adds a pseudocount
#' to each feature in each module. Only used if \code{yInit} is set. Default 1.
#' @param gamma Numeric. Concentration parameter for Eta. Adds a pseudocount
#' to the number of features in each module. Only used if \code{yInit} is set.
#' Default 1.
#' @param minCell Integer. Only attempt to split cell populations with at
#' least this many cells.
#' @param reorder Logical. Whether to reorder cell populations using
#' hierarchical clustering after each model has been created. If FALSE, cell
#' populations numbers will correspond to the split which created the cell
#' populations (i.e. 'K15' was created at split 15, 'K16' was created at split
#' 16, etc.). Default TRUE.
#' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,
#' a default value of 12345 is used. If NULL, no calls to
#' \link[withr]{with_seed} are made.
#' @param perplexity Logical. Whether to calculate perplexity for each model.
#' If FALSE, then perplexity can be calculated later with
#' \link{resamplePerplexity}. Default TRUE.
#' @param verbose Logical. Whether to print log messages. Default TRUE.
#' @param logfile Character. Messages will be redirected to a file named
#' "logfile". If NULL, messages will be printed to stdout. Default NULL.
#' @param ... Ignored. Placeholder to prevent check warning.
#' @return A \linkS4class{SingleCellExperiment} object. Function
#' parameter settings and celda model results are stored in the
#' \link{metadata} \code{"celda_grid_search"} slot. The models in
#' the list will be of class \code{celda_C} if \code{yInit = NULL} or
#' \code{celda_CG} if \code{zInit} is set.
#' @seealso \link{recursiveSplitModule} for recursive splitting of feature
#' modules.
#' @export
setGeneric("recursiveSplitCell", function(x, ...) {
standardGeneric("recursiveSplitCell")})
#' @rdname recursiveSplitCell
#' @examples
#' data(sceCeldaCG)
#' ## Create models that range from K = 3 to K = 7 by recursively splitting
#' ## cell populations into two to produce \link{celda_C} cell clustering models
#' sce <- recursiveSplitCell(sceCeldaCG, initialK = 3, maxK = 7)
#'
#' ## Alternatively, first identify features modules using
#' ## \link{recursiveSplitModule}
#' moduleSplit <- recursiveSplitModule(sceCeldaCG, initialL = 3, maxL = 15)
#' plotGridSearchPerplexity(moduleSplit)
#' moduleSplitSelect <- subsetCeldaList(moduleSplit, list(L = 10))
#'
#' ## Then use module labels for initialization in \link{recursiveSplitCell} to
#' ## produce \link{celda_CG} bi-clustering models
#' cellSplit <- recursiveSplitCell(sceCeldaCG,
#' initialK = 3, maxK = 7, yInit = celdaModules(moduleSplitSelect))
#' plotGridSearchPerplexity(cellSplit)
#' sce <- subsetCeldaList(cellSplit, list(K = 5, L = 10))
#' @export
setMethod("recursiveSplitCell",
signature(x = "SingleCellExperiment"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
sampleLabel = NULL,
initialK = 5,
maxK = 25,
tempL = NULL,
yInit = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minCell = 3,
reorder = TRUE,
seed = 12345,
perplexity = TRUE,
logfile = NULL,
verbose = TRUE) {
xClass <- "SingleCellExperiment"
if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {
stop(altExpName, " not in 'altExpNames(x)'. Run ",
"selectFeatures(x) first!")
}
altExp <- SingleCellExperiment::altExp(x, altExpName)
if (!useAssay %in% SummarizedExperiment::assayNames(altExp)) {
stop(useAssay, " not in assayNames(altExp(x, altExpName))")
}
counts <- SummarizedExperiment::assay(altExp, i = useAssay)
if (!is.null(yInit)) {
model <- "celda_CG"
} else {
model <- "celda_C"
}
celdaList <- .recursiveSplitCellWithSeed(counts = counts,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
altExp <- .createSCERecursiveSplitCell(celdaList = celdaList,
sce = altExp,
xClass = xClass,
useAssay = useAssay,
model = model,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
}
)
#' @rdname recursiveSplitCell
#' @examples
#' data(celdaCGSim, celdaCSim)
#' ## Create models that range from K = 3 to K = 7 by recursively splitting
#' ## cell populations into two to produce \link{celda_C} cell clustering models
#' sce <- recursiveSplitCell(celdaCSim$counts, initialK = 3, maxK = 7)
#'
#' ## Alternatively, first identify features modules using
#' ## \link{recursiveSplitModule}
#' moduleSplit <- recursiveSplitModule(celdaCGSim$counts,
#' initialL = 3, maxL = 15)
#' plotGridSearchPerplexity(moduleSplit)
#' moduleSplitSelect <- subsetCeldaList(moduleSplit, list(L = 10))
#'
#' ## Then use module labels for initialization in \link{recursiveSplitCell} to
#' ## produce \link{celda_CG} bi-clustering models
#' cellSplit <- recursiveSplitCell(celdaCGSim$counts,
#' initialK = 3, maxK = 7, yInit = celdaModules(moduleSplitSelect))
#' plotGridSearchPerplexity(cellSplit)
#' sce <- subsetCeldaList(cellSplit, list(K = 5, L = 10))
#' @export
setMethod("recursiveSplitCell",
signature(x = "matrix"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
sampleLabel = NULL,
initialK = 5,
maxK = 25,
tempL = NULL,
yInit = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minCell = 3,
reorder = TRUE,
seed = 12345,
perplexity = TRUE,
logfile = NULL,
verbose = TRUE) {
ls <- list()
ls[[useAssay]] <- x
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)
SingleCellExperiment::altExp(sce, altExpName) <- sce
xClass <- "matrix"
if (!is.null(yInit)) {
model <- "celda_CG"
} else {
model <- "celda_C"
}
celdaList <- .recursiveSplitCellWithSeed(counts = x,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
altExp <- .createSCERecursiveSplitCell(celdaList = celdaList,
sce = SingleCellExperiment::altExp(sce, altExpName),
xClass = xClass,
useAssay = useAssay,
model = model,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
SingleCellExperiment::altExp(sce, altExpName) <- altExp
return(sce)
}
)
.recursiveSplitCellWithSeed <- function(counts,
sampleLabel,
initialK,
maxK,
tempL,
yInit,
alpha,
beta,
delta,
gamma,
minCell,
reorder,
seed,
perplexity,
logfile,
verbose) {
if (is.null(seed)) {
celdaList <- .recursiveSplitCell(counts = counts,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
} else {
with_seed(
seed,
celdaList <- .recursiveSplitCell(counts = counts,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
)
}
return(celdaList)
}
.recursiveSplitCell <- function(counts,
sampleLabel,
initialK,
maxK,
tempL,
yInit,
alpha,
beta,
delta,
gamma,
minCell,
reorder,
perplexity,
logfile,
verbose) {
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = FALSE,
verbose = verbose
)
.logMessages("Starting recursive cell population splitting.",
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.validateCounts(counts)
startTime <- Sys.time()
counts <- .processCounts(counts)
countChecksum <- .createCountChecksum(counts)
sampleLabel <- .processSampleLabels(sampleLabel, numCells = ncol(counts))
s <- as.integer(sampleLabel)
names <- list(
row = rownames(counts),
column = colnames(counts),
sample = levels(sampleLabel)
)
if (!is.null(yInit)) {
# Create collapsed module matrix
L <- length(unique(yInit))
.logMessages(date(),
".. Collapsing to",
L,
"modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
overallY <- .initializeCluster(L, nrow(counts), initial = yInit)
countsY <- .rowSumByGroup(counts, overallY, L)
# Create initial model with initialK and predifined y labels
.logMessages(date(),
".. Initializing with",
initialK,
"populations",
append = TRUE,
verbose = verbose,
logfile = logfile)
modelInitial <- .celda_CG(counts,
sampleLabel = s,
K = as.integer(initialK),
L = as.integer(L),
zInitialize = "split",
yInitialize = "predefined",
nchains = 1,
yInit = overallY,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
verbose = FALSE,
reorder = reorder)
currentK <- length(unique(celdaClusters(modelInitial)$z)) + 1
overallZ <- celdaClusters(modelInitial)$z
resList <- list(modelInitial)
while (currentK <= maxK) {
# previousY <- overallY
tempSplit <- .singleSplitZ(countsY,
overallZ,
s,
currentK,
minCell = 3,
alpha = alpha,
beta = beta
)
tempModel <- .celda_CG(counts,
sampleLabel = s,
K = as.integer(currentK),
L = as.integer(L),
yInit = overallY,
zInit = tempSplit$z,
nchains = 1,
zInitialize = "predefined",
yInitialize = "predefined",
splitOnLast = FALSE,
stopIter = 5,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
verbose = FALSE,
reorder = reorder
)
# Calculate new decomposed counts matrix with new module labels
# overallY = clusters(tempModel)$y
# p = .cGReDecomposeCounts(counts, overallY, previousY, countsY,
# nByG, L = as.integer(L))
# countsY = p$nTSByC
# If the number of clusters is still "currentK", then keep the
# reordering, otherwise keep the previous configuration
if (length(unique(celdaClusters(tempModel)$z)) == currentK) {
overallZ <- celdaClusters(tempModel)$z
} else {
overallZ <- tempSplit$z
ll <- .logLikelihoodcelda_CG(
counts,
s,
overallZ,
celdaClusters(tempModel)$y,
currentK,
L,
alpha,
beta,
delta,
gamma
)
tempModel <- methods::new("celda_CG",
clusters = list(z = overallZ, y = celdaClusters(tempModel)$y),
params = list(
K = as.integer(currentK),
L = as.integer(L),
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
countChecksum = countChecksum
),
finalLogLik = ll,
sampleLabel = sampleLabel,
names = names
)
}
resList <- c(resList, list(tempModel))
.logMessages(date(),
".. Current cell population",
currentK,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = logfile
)
currentK <- length(unique(overallZ)) + 1
}
runK <- vapply(resList, function(mod) {
params(mod)$K
}, integer(1))
runL <- vapply(resList, function(mod) {
params(mod)$L
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
L = as.integer(runL),
K = as.integer(runK),
stringsAsFactors = FALSE
)
} else if (!is.null(tempL)) {
L <- tempL
.logMessages(date(),
".. Collapsing to",
L,
"temporary modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
tempY <- .initializeSplitY(counts,
L = as.integer(L),
tempK = max(100, maxK),
minFeature = 3
)
tempY <- as.integer(as.factor(tempY))
L <- length(unique(tempY)) # Recalculate in case some modules are empty
countsY <- .rowSumByGroup(counts, tempY, L)
# Create initial model with initialK
.logMessages(date(),
".. Initializing with",
initialK,
"populations",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_C(countsY,
sampleLabel = s,
K = as.integer(initialK),
zInitialize = "split",
nchains = 1,
alpha = alpha,
beta = beta,
verbose = FALSE,
reorder = reorder
)
currentK <- length(unique(celdaClusters(modelInitial)$z)) + 1
overallZ <- celdaClusters(modelInitial)$z
ll <- .logLikelihoodcelda_C(
counts, s, overallZ, currentK,
alpha, beta
)
modelInitial@params$countChecksum <- countChecksum
modelInitial@completeLogLik <- ll
modelInitial@finalLogLik <- ll
resList <- list(modelInitial)
while (currentK <= maxK) {
# Find next best split, then do a new celda_C run with that split
tempSplit <- .singleSplitZ(countsY,
overallZ,
s,
currentK,
minCell = 3,
alpha = alpha,
beta = beta
)
tempModel <- .celda_C(countsY,
sampleLabel = s,
K = as.integer(currentK),
nchains = 1,
zInitialize = "random",
alpha = alpha,
beta = beta,
stopIter = 5,
splitOnLast = FALSE,
verbose = FALSE,
zInit = tempSplit$z,
reorder = reorder
)
# Handle rare cases where a population has no cells after running
# the model
if (length(unique(celdaClusters(tempModel)$z)) == currentK) {
overallZ <- celdaClusters(tempModel)$z
} else {
overallZ <- tempSplit$z
}
# Need to change below line to use decompose counts to save time
ll <- .logLikelihoodcelda_C(
counts, s, overallZ, currentK,
alpha, beta
)
tempModel <- methods::new("celda_C",
clusters = list(z = overallZ),
params = list(
K = as.integer(currentK),
alpha = alpha,
beta = beta,
countChecksum = countChecksum
),
finalLogLik = ll,
sampleLabel = sampleLabel,
names = names
)
resList <- c(resList, list(tempModel))
.logMessages(date(),
".. Current cell population",
currentK,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = logfile
)
currentK <- length(unique(overallZ)) + 1
}
runK <- vapply(resList, function(mod) {
params(mod)$K
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
K = as.integer(runK),
stringsAsFactors = FALSE
)
} else {
# Create initial model with initialK
.logMessages(date(),
".. Initializing with",
initialK,
"populations",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_C(counts,
sampleLabel = s,
K = as.integer(initialK),
zInitialize = "split",
nchains = 1,
alpha = alpha,
beta = beta,
verbose = FALSE,
reorder = reorder
)
currentK <- length(unique(celdaClusters(modelInitial)$z)) + 1
overallZ <- celdaClusters(modelInitial)$z
resList <- list(modelInitial)
while (currentK <= maxK) {
tempSplit <- .singleSplitZ(counts,
overallZ,
s,
currentK,
minCell = 3,
alpha = alpha,
beta = beta
)
tempModel <- .celda_C(counts,
sampleLabel = s,
K = as.integer(currentK),
nchains = 1,
zInitialize = "random",
alpha = alpha,
beta = beta,
stopIter = 5,
splitOnLast = FALSE,
verbose = FALSE,
zInit = tempSplit$z,
reorder = reorder
)
if (length(unique(celdaClusters(tempModel)$z)) == currentK) {
overallZ <- celdaClusters(tempModel)$z
} else {
overallZ <- tempSplit$z
ll <-
.logLikelihoodcelda_C(
counts, s, overallZ,
currentK, alpha, beta
)
tempModel <- methods::new("celda_C",
clusters = list(z = overallZ),
params = list(
K = as.integer(currentK),
alpha = alpha,
beta = beta,
countChecksum = countChecksum
),
finalLogLik = ll,
sampleLabel = sampleLabel,
names = names
)
}
resList <- c(resList, list(tempModel))
.logMessages(date(),
".. Current cell population",
currentK,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = logfile
)
currentK <- length(unique(overallZ)) + 1
}
runK <- vapply(resList, function(mod) {
params(mod)$K
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
K = as.integer(runK),
stringsAsFactors = FALSE
)
}
# Summarize paramters of different models
logliks <- vapply(resList, function(mod) {
bestLogLikelihood(mod)
}, double(1))
runParams <- data.frame(runParams,
log_likelihood = logliks,
stringsAsFactors = FALSE
)
celdaRes <- methods::new("celdaList",
runParams = runParams,
resList = resList,
countChecksum = countChecksum
)
if (isTRUE(perplexity)) {
.logMessages(date(),
".. Calculating perplexity",
append = TRUE,
verbose = verbose,
logfile = NULL
)
celdaRes <- resamplePerplexity(counts, celdaRes)
}
endTime <- Sys.time()
.logMessages(
paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(
"Completed recursive cell population splitting. Total time:",
format(difftime(endTime, startTime)),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(
paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
return(celdaRes)
}
#' @title Recursive module splitting
#' @description Uses the \link{celda_G} model to cluster features into modules
#' for a range of possible L's. The module labels of the previous "L-1" model
#' are used as the initial values in the current model with L modules. The best
#' split of an existing module is found to create the L-th module. This
#' procedure is much faster than randomly initializing each model with a
#' different L.
#' @param x A numeric \link{matrix} of counts or a
#' \linkS4class{SingleCellExperiment}
#' with the matrix located in the assay slot under \code{useAssay}.
#' Rows represent features and columns represent cells.
#' @param useAssay A string specifying which \link{assay}
#' slot to use if \code{x} is a
#' \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param initialL Integer. Minimum number of modules to try.
#' @param maxL Integer. Maximum number of modules to try.
#' @param tempK Integer. Number of temporary cell populations to identify and
#' use in module splitting. Only used if \code{zInit = NULL} Collapsing cells
#' to a relatively smaller number of cell popluations will increase the
#' speed of module clustering and tend to produce better modules. This number
#' should be larger than the number of true cell populations expected in the
#' dataset. Default 100.
#' @param zInit Integer vector. Collapse cells to cell populations based on
#' labels in \code{zInit} and then perform module splitting. If NULL, no
#' collapasing will be performed unless \code{tempK} is specified.
#' Default NULL.
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell
#' (column) in the count matrix. Only used if \code{zInit} is set.
#' @param alpha Numeric. Concentration parameter for Theta. Adds a pseudocount
#' to each cell population in each sample. Only used if \code{zInit} is set.
#' Default 1.
#' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount
#' to each feature module in each cell. Default 1.
#' @param delta Numeric. Concentration parameter for Psi. Adds a pseudocount
#' to each feature in each module. Default 1.
#' @param gamma Numeric. Concentration parameter for Eta. Adds a pseudocount
#' to the number of features in each module. Default 1.
#' @param minFeature Integer. Only attempt to split modules with at least this
#' many features.
#' @param reorder Logical. Whether to reorder modules using hierarchical
#' clustering after each model has been created. If FALSE, module numbers will
#' correspond to the split which created the module (i.e. 'L15' was created at
#' split 15, 'L16' was created at split 16, etc.). Default TRUE.
#' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,
#' a default value of 12345 is used. If NULL, no calls to
#' \link[withr]{with_seed} are made.
#' @param perplexity Logical. Whether to calculate perplexity for each model.
#' If FALSE, then perplexity can be calculated later with
#' \link{resamplePerplexity}. Default TRUE.
#' @param verbose Logical. Whether to print log messages. Default TRUE.
#' @param logfile Character. Messages will be redirected to a file named
#' "logfile". If NULL, messages will be printed to stdout. Default NULL.
#' @param ... Ignored. Placeholder to prevent check warning.
#' @return A \linkS4class{SingleCellExperiment} object. Function
#' parameter settings and celda model results are stored in the
#' \link{metadata} \code{"celda_grid_search"} slot. The models in
#' the list will be of class \link{celda_G} if \code{zInit = NULL} or
#' \link{celda_CG} if \code{zInit} is set.
#' @seealso \code{recursiveSplitCell} for recursive splitting of cell
#' populations.
#' @export
setGeneric("recursiveSplitModule", function(x, ...) {
standardGeneric("recursiveSplitModule")})
#' @rdname recursiveSplitModule
#' @examples
#' data(sceCeldaCG)
#' ## Create models that range from L=3 to L=20 by recursively splitting modules
#' ## into two
#' moduleSplit <- recursiveSplitModule(sceCeldaCG, initialL = 3, maxL = 20)
#'
#' ## Example results with perplexity
#' plotGridSearchPerplexity(moduleSplit)
#'
#' ## Select model for downstream analysis
#' celdaMod <- subsetCeldaList(moduleSplit, list(L = 10))
#' @export
setMethod("recursiveSplitModule",
signature(x = "SingleCellExperiment"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
initialL = 10,
maxL = 100,
tempK = 100,
zInit = NULL,
sampleLabel = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minFeature = 3,
reorder = TRUE,
seed = 12345,
perplexity = TRUE,
verbose = TRUE,
logfile = NULL) {
xClass <- "SingleCellExperiment"
if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {
stop(altExpName, " not in 'altExpNames(x)'. Run ",
"selectFeatures(x) first!")
}
altExp <- SingleCellExperiment::altExp(x, altExpName)
if (!useAssay %in% SummarizedExperiment::assayNames(altExp)) {
stop(useAssay, " not in assayNames(altExp(x, altExpName))")
}
counts <- SummarizedExperiment::assay(altExp, i = useAssay)
if (!is.null(zInit)) {
model <- "celda_CG"
} else {
model <- "celda_G"
}
celdaList <- .recursiveSplitModuleWithSeed(counts = counts,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
altExp <- .createSCERecursiveSplitModule(celdaList = celdaList,
sce = altExp,
xClass = xClass,
useAssay = useAssay,
model = model,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
}
)
#' @rdname recursiveSplitModule
#' @examples
#' data(celdaCGSim)
#' ## Create models that range from L=3 to L=20 by recursively splitting modules
#' ## into two
#' moduleSplit <- recursiveSplitModule(celdaCGSim$counts,
#' initialL = 3, maxL = 20)
#'
#' ## Example results with perplexity
#' plotGridSearchPerplexity(moduleSplit)
#'
#' ## Select model for downstream analysis
#' celdaMod <- subsetCeldaList(moduleSplit, list(L = 10))
#' @export
setMethod("recursiveSplitModule",
signature(x = "matrix"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
initialL = 10,
maxL = 100,
tempK = 100,
zInit = NULL,
sampleLabel = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minFeature = 3,
reorder = TRUE,
seed = 12345,
perplexity = TRUE,
verbose = TRUE,
logfile = NULL) {
ls <- list()
ls[[useAssay]] <- x
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)
SingleCellExperiment::altExp(sce, altExpName) <- sce
xClass <- "matrix"
if (!is.null(zInit)) {
model <- "celda_CG"
} else {
model <- "celda_G"
}
celdaList <- .recursiveSplitModuleWithSeed(counts = x,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
altExp <- .createSCERecursiveSplitModule(celdaList = celdaList,
sce = SingleCellExperiment::altExp(sce, altExpName),
xClass = xClass,
useAssay = useAssay,
model = model,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
SingleCellExperiment::altExp(sce, altExpName) <- altExp
return(sce)
}
)
.recursiveSplitModuleWithSeed <- function(counts,
initialL,
maxL,
tempK,
zInit,
sampleLabel,
alpha,
beta,
delta,
gamma,
minFeature,
reorder,
seed,
perplexity,
verbose,
logfile) {
if (is.null(seed)) {
celdaList <- .recursiveSplitModule(
counts = counts,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
} else {
with_seed(seed,
celdaList <- .recursiveSplitModule(
counts = counts,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
)
}
return(celdaList)
}
.recursiveSplitModule <- function(counts,
initialL = 10,
maxL = 100,
tempK = 100,
zInit = NULL,
sampleLabel = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minFeature = 3,
reorder = TRUE,
perplexity = TRUE,
verbose = TRUE,
logfile = NULL) {
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = FALSE,
verbose = verbose
)
.logMessages("Starting recursive module splitting.",
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
startTime <- Sys.time()
.validateCounts(counts)
counts <- .processCounts(counts)
countChecksum <- .createCountChecksum(counts)
names <-
list(row = rownames(counts), column = colnames(counts))
sampleLabel <- .processSampleLabels(sampleLabel,
numCells = ncol(counts)
)
s <- as.integer(sampleLabel)
if (!is.null(zInit)) {
# Create collapsed module matrix
K <- length(unique(zInit))
.logMessages(
date(),
".. Collapsing to",
K,
"cell populations",
append = TRUE,
verbose = verbose,
logfile = logfile
)
overallZ <- .initializeCluster(
N = K,
len = ncol(counts),
initial = zInit
)
countsZ <- .colSumByGroup(counts, overallZ, K)
# Create initial model with initialL and predifined z labels
.logMessages(date(),
".. Initializing with",
initialL,
"modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_CG(counts,
sampleLabel = s,
L = initialL,
K = K,
zInitialize = "predefined",
yInitialize = "split",
nchains = 1,
zInit = overallZ,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
verbose = FALSE,
reorder = reorder)
currentL <- length(unique(celdaClusters(modelInitial)$y)) + 1
overallY <- celdaClusters(modelInitial)$y
resList <- list(modelInitial)
while (currentL <= maxL) {
# Allow features to cluster further with celda_CG
tempSplit <- .singleSplitY(
countsZ,
overallY,
currentL,
minFeature = 3,
beta = beta,
delta = delta,
gamma = gamma
)
tempModel <- .celda_CG(
counts,
L = currentL,
K = K,
stopIter = 5,
splitOnIter = -1,
splitOnLast = FALSE,
nchains = 1,
verbose = FALSE,
yInitialize = "predefined",
zInitialize = "predefined",
yInit = tempSplit$y,
zInit = overallZ,
reorder = reorder
)
overallY <- celdaClusters(tempModel)$y
## Add new model to results list and increment L
.logMessages(
date(),
".. Created module",
currentL,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = NULL
)
resList <- c(resList, list(tempModel))
currentL <- currentL + 1
}
runK <- vapply(resList, function(mod) {
params(mod)$K
}, integer(1))
runL <- vapply(resList, function(mod) {
params(mod)$L
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
L = runL,
K = runK,
stringsAsFactors = FALSE
)
} else if (!is.null(tempK)) {
K <- tempK
.logMessages(
date(),
".. Collapsing to",
K,
"temporary cell populations",
append = TRUE,
verbose = verbose,
logfile = logfile
)
z <- .initializeSplitZ(counts,
K = K,
minCell = 3
)
countsZ <- .colSumByGroup(counts, z, length(unique(z)))
.logMessages(
date(),
".. Initializing with",
initialL,
"modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_G(
countsZ,
L = initialL,
nchains = 1,
verbose = FALSE
)
currentL <- length(unique(celdaClusters(modelInitial)$y)) + 1
overallY <- celdaClusters(modelInitial)$y
## Decomposed counts for full count matrix
p <- .cGDecomposeCounts(counts, overallY, currentL)
nTSByC <- p$nTSByC
nByTS <- p$nByTS
nGByTS <- p$nGByTS
nByG <- p$nByG
nG <- p$nG
nM <- p$nM
resList <- list(modelInitial)
while (currentL <= maxL) {
# Allow features to cluster further
previousY <- overallY
tempSplit <- .singleSplitY(
countsZ,
overallY,
currentL,
minFeature = 3,
beta = beta,
delta = delta,
gamma = gamma
)
tempModel <- .celda_G(
countsZ,
L = currentL,
stopIter = 5,
splitOnIter = -1,
splitOnLast = FALSE,
nchains = 1,
verbose = FALSE,
yInitialize = "predefined",
yInit = tempSplit$y,
reorder = reorder
)
overallY <- celdaClusters(tempModel)$y
# Adjust decomposed count matrices
p <- .cGReDecomposeCounts(counts,
overallY,
previousY,
nTSByC,
nByG,
L = currentL
)
nTSByC <- p$nTSByC
nByTS <- p$nByTS
nGByTS <- p$nGByTS
previousY <- overallY
## Create the final model object with correct info on full counts
## matrix
tempModel@finalLogLik <- .cGCalcLL(
nTSByC = nTSByC,
nByTS = nByTS,
nByG = nByG,
nGByTS = nGByTS,
nM = nM,
nG = nG,
L = currentL,
beta = beta,
delta = delta,
gamma = gamma
)
tempModel@completeLogLik <- bestLogLikelihood(tempModel)
tempModel@params$countChecksum <- countChecksum
tempModel@names <- names
## Add extra row/column for next round of L
nTSByC <- rbind(nTSByC, rep(0L, ncol(nTSByC)))
nByTS <- c(nByTS, 0L)
nGByTS <- c(nGByTS, 0L)
## Add new model to results list and increment L
.logMessages(
date(),
".. Created module",
currentL,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = NULL
)
resList <- c(resList, list(tempModel))
currentL <- currentL + 1
}
runL <- vapply(resList, function(mod) {
params(mod)$L
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
L = runL,
stringsAsFactors = FALSE
)
} else {
.logMessages(
date(),
".. Initializing with",
initialL,
"modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_G(
counts,
L = initialL,
maxIter = 20,
nchains = 1,
verbose = FALSE
)
overallY <- celdaClusters(modelInitial)$y
currentL <- length(unique(overallY)) + 1
## Perform splitting for y labels
resList <- list(modelInitial)
while (currentL <= maxL) {
# Allow features to cluster further
previousY <- overallY
tempSplit <- .singleSplitY(
counts,
overallY,
currentL,
minFeature = 3,
beta = beta,
delta = delta,
gamma = gamma
)
tempModel <- .celda_G(
counts,
L = currentL,
stopIter = 5,
splitOnIter = -1,
splitOnLast = FALSE,
nchains = 1,
verbose = FALSE,
yInitialize = "predefined",
yInit = tempSplit$y,
reorder = reorder
)
overallY <- celdaClusters(tempModel)$y
## Add new model to results list and increment L
.logMessages(
date(),
".. Created module",
currentL,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = NULL
)
resList <- c(resList, list(tempModel))
currentL <- currentL + 1
}
runL <- vapply(resList, function(mod) {
params(mod)$L
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
L = runL,
stringsAsFactors = FALSE
)
}
## Summarize paramters of different models
logliks <- vapply(resList, function(mod) {
bestLogLikelihood(mod)
}, double(1))
runParams <- data.frame(runParams,
log_likelihood = logliks,
stringsAsFactors = FALSE
)
celdaRes <- methods::new(
"celdaList",
runParams = runParams,
resList = resList,
countChecksum = countChecksum
)
if (isTRUE(perplexity)) {
.logMessages(
date(),
".. Calculating perplexity",
append = TRUE,
verbose = verbose,
logfile = NULL
)
celdaRes <- resamplePerplexity(counts, celdaRes)
}
endTime <- Sys.time()
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages("Completed recursive module splitting. Total time:",
format(difftime(endTime, startTime)),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
return(celdaRes)
}
.createSCERecursiveSplitCell <- function(celdaList,
sce,
xClass,
useAssay,
model,
sampleLabel,
initialK,
maxK,
tempL,
yInit,
alpha,
beta,
delta,
gamma,
minCell,
reorder,
seed,
perplexity,
logfile,
verbose) {
S4Vectors::metadata(sce)[["celda_grid_search"]] <- celdaList
S4Vectors::metadata(sce)$celda_grid_search@celdaGridSearchParameters <-
list(xClass = xClass,
useAssay = useAssay,
model = model,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
return(sce)
}
.createSCERecursiveSplitModule <- function(celdaList,
sce,
xClass,
useAssay,
model,
initialL,
maxL,
tempK,
zInit,
sampleLabel,
alpha,
beta,
delta,
gamma,
minFeature,
reorder,
seed,
perplexity,
verbose,
logfile) {
S4Vectors::metadata(sce)[["celda_grid_search"]] <- celdaList
S4Vectors::metadata(sce)$celda_grid_search@celdaGridSearchParameters <-
list(xClass = xClass,
useAssay = useAssay,
model = model,
sampleLabel = sampleLabel,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
return(sce)
}
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Defines functions .createSCERecursiveSplitModule .createSCERecursiveSplitCell .recursiveSplitModule .recursiveSplitModuleWithSeed .recursiveSplitCell .recursiveSplitCellWithSeed .singleSplitY .singleSplitZ
.singleSplitZ <- function(counts,
z,
s,
K,
minCell = 3,
alpha = 1,
beta = 1) {
zTa <- tabulate(z, K)
zToSplit <- which(zTa > minCell)
bestZ <- z
bestLl <- -Inf
for (i in zToSplit) {
clustLabel <- .celda_C(
counts[, z == i, drop = FALSE],
K = 2,
zInitialize = "random",
splitOnIter = -1,
splitOnLast = FALSE,
verbose = FALSE
)
if (length(unique(celdaClusters(clustLabel)$z)) == 2) {
ix <- z == i
newZ <- z
newZ[ix] <- ifelse(celdaClusters(clustLabel)$z == 2, i, K)
ll <- .logLikelihoodcelda_C(counts, s, newZ, K, alpha, beta)
if (ll > bestLl) {
bestZ <- newZ
bestLl <- ll
}
}
}
return(list(ll = bestLl, z = bestZ))
}
.singleSplitY <- function(counts,
y,
L,
minFeature = 3,
beta = 1,
delta = 1,
gamma = 1) {
yTa <- tabulate(y, L)
yToSplit <- which(yTa > minFeature)
bestY <- y
bestLl <- -Inf
# previousY <- y
for (i in yToSplit) {
clustLabel <- .celda_G(counts[y == i, , drop = FALSE],
L = 2,
yInitialize = "random",
splitOnIter = -1,
splitOnLast = FALSE,
nchains = 1,
verbose = FALSE
)
if (length(unique(celdaClusters(clustLabel)$y)) == 2) {
ix <- y == i
newY <- y
newY[ix] <- ifelse(celdaClusters(clustLabel)$y == 2, i, L)
ll <- .logLikelihoodcelda_G(counts, newY, L, beta, delta, gamma)
if (ll > bestLl) {
bestY <- newY
bestLl <- ll
}
}
}
return(list(ll = bestLl, y = bestY))
}
#' @title Recursive cell splitting
#' @description Uses the \link{celda_C} model to cluster cells into
#' population for range of possible K's. The cell population labels of the
#' previous "K-1" model are used as the initial values in the current model
#' with K cell populations. The best split of an existing cell population is
#' found to create the K-th cluster. This procedure is much faster than
#' randomly initializing each model with a different K. If module labels for
#' each feature are given in 'yInit', the \link{celda_CG} model will be used to
#' split cell populations based on those modules instead of individual
#' features. Module labels will also be updated during sampling and thus
#' may end up slightly different than \code{yInit}.
#' @param x A numeric \link{matrix} of counts or a
#' \linkS4class{SingleCellExperiment}
#' with the matrix located in the assay slot under \code{useAssay}.
#' Rows represent features and columns represent cells.
#' @param useAssay A string specifying the name of the
#' \link{assay}
#' slot to use. Default "counts".
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell
#' (column) in the count matrix.
#' @param initialK Integer. Minimum number of cell populations to try.
#' @param maxK Integer. Maximum number of cell populations to try.
#' @param tempL Integer. Number of temporary modules to identify and use in cell
#' splitting. Only used if \code{yInit = NULL}. Collapsing features to a
#' relatively smaller number of modules will increase the speed of clustering
#' and tend to produce better cell populations. This number should be larger
#' than the number of true modules expected in the dataset. Default NULL.
#' @param yInit Integer vector. Module labels for features. Cells will be
#' clustered using the \link{celda_CG} model based on the modules specified in
#' \code{yInit} rather than the counts of individual features. While the
#' features will be initialized to the module labels in \code{yInit}, the
#' labels will be allowed to move within each new model with a different K.
#' @param alpha Numeric. Concentration parameter for Theta. Adds a pseudocount
#' to each cell population in each sample. Default 1.
#' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount to
#' each feature in each cell (if \code{yInit} is NULL) or to each module in
#' each cell population (if \code{yInit} is set). Default 1.
#' @param delta Numeric. Concentration parameter for Psi. Adds a pseudocount
#' to each feature in each module. Only used if \code{yInit} is set. Default 1.
#' @param gamma Numeric. Concentration parameter for Eta. Adds a pseudocount
#' to the number of features in each module. Only used if \code{yInit} is set.
#' Default 1.
#' @param minCell Integer. Only attempt to split cell populations with at
#' least this many cells.
#' @param reorder Logical. Whether to reorder cell populations using
#' hierarchical clustering after each model has been created. If FALSE, cell
#' populations numbers will correspond to the split which created the cell
#' populations (i.e. 'K15' was created at split 15, 'K16' was created at split
#' 16, etc.). Default TRUE.
#' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,
#' a default value of 12345 is used. If NULL, no calls to
#' \link[withr]{with_seed} are made.
#' @param perplexity Logical. Whether to calculate perplexity for each model.
#' If FALSE, then perplexity can be calculated later with
#' \link{resamplePerplexity}. Default TRUE.
#' @param verbose Logical. Whether to print log messages. Default TRUE.
#' @param logfile Character. Messages will be redirected to a file named
#' "logfile". If NULL, messages will be printed to stdout. Default NULL.
#' @param ... Ignored. Placeholder to prevent check warning.
#' @return A \linkS4class{SingleCellExperiment} object. Function
#' parameter settings and celda model results are stored in the
#' \link{metadata} \code{"celda_grid_search"} slot. The models in
#' the list will be of class \code{celda_C} if \code{yInit = NULL} or
#' \code{celda_CG} if \code{zInit} is set.
#' @seealso \link{recursiveSplitModule} for recursive splitting of feature
#' modules.
#' @export
setGeneric("recursiveSplitCell", function(x, ...) {
standardGeneric("recursiveSplitCell")})
#' @rdname recursiveSplitCell
#' @examples
#' data(sceCeldaCG)
#' ## Create models that range from K = 3 to K = 7 by recursively splitting
#' ## cell populations into two to produce \link{celda_C} cell clustering models
#' sce <- recursiveSplitCell(sceCeldaCG, initialK = 3, maxK = 7)
#'
#' ## Alternatively, first identify features modules using
#' ## \link{recursiveSplitModule}
#' moduleSplit <- recursiveSplitModule(sceCeldaCG, initialL = 3, maxL = 15)
#' plotGridSearchPerplexity(moduleSplit)
#' moduleSplitSelect <- subsetCeldaList(moduleSplit, list(L = 10))
#'
#' ## Then use module labels for initialization in \link{recursiveSplitCell} to
#' ## produce \link{celda_CG} bi-clustering models
#' cellSplit <- recursiveSplitCell(sceCeldaCG,
#' initialK = 3, maxK = 7, yInit = celdaModules(moduleSplitSelect))
#' plotGridSearchPerplexity(cellSplit)
#' sce <- subsetCeldaList(cellSplit, list(K = 5, L = 10))
#' @export
setMethod("recursiveSplitCell",
signature(x = "SingleCellExperiment"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
sampleLabel = NULL,
initialK = 5,
maxK = 25,
tempL = NULL,
yInit = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minCell = 3,
reorder = TRUE,
seed = 12345,
perplexity = TRUE,
logfile = NULL,
verbose = TRUE) {
xClass <- "SingleCellExperiment"
if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {
stop(altExpName, " not in 'altExpNames(x)'. Run ",
"selectFeatures(x) first!")
}
altExp <- SingleCellExperiment::altExp(x, altExpName)
if (!useAssay %in% SummarizedExperiment::assayNames(altExp)) {
stop(useAssay, " not in assayNames(altExp(x, altExpName))")
}
counts <- SummarizedExperiment::assay(altExp, i = useAssay)
if (!is.null(yInit)) {
model <- "celda_CG"
} else {
model <- "celda_C"
}
celdaList <- .recursiveSplitCellWithSeed(counts = counts,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
altExp <- .createSCERecursiveSplitCell(celdaList = celdaList,
sce = altExp,
xClass = xClass,
useAssay = useAssay,
model = model,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
}
)
#' @rdname recursiveSplitCell
#' @examples
#' data(celdaCGSim, celdaCSim)
#' ## Create models that range from K = 3 to K = 7 by recursively splitting
#' ## cell populations into two to produce \link{celda_C} cell clustering models
#' sce <- recursiveSplitCell(celdaCSim$counts, initialK = 3, maxK = 7)
#'
#' ## Alternatively, first identify features modules using
#' ## \link{recursiveSplitModule}
#' moduleSplit <- recursiveSplitModule(celdaCGSim$counts,
#' initialL = 3, maxL = 15)
#' plotGridSearchPerplexity(moduleSplit)
#' moduleSplitSelect <- subsetCeldaList(moduleSplit, list(L = 10))
#'
#' ## Then use module labels for initialization in \link{recursiveSplitCell} to
#' ## produce \link{celda_CG} bi-clustering models
#' cellSplit <- recursiveSplitCell(celdaCGSim$counts,
#' initialK = 3, maxK = 7, yInit = celdaModules(moduleSplitSelect))
#' plotGridSearchPerplexity(cellSplit)
#' sce <- subsetCeldaList(cellSplit, list(K = 5, L = 10))
#' @export
setMethod("recursiveSplitCell",
signature(x = "matrix"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
sampleLabel = NULL,
initialK = 5,
maxK = 25,
tempL = NULL,
yInit = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minCell = 3,
reorder = TRUE,
seed = 12345,
perplexity = TRUE,
logfile = NULL,
verbose = TRUE) {
ls <- list()
ls[[useAssay]] <- x
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)
SingleCellExperiment::altExp(sce, altExpName) <- sce
xClass <- "matrix"
if (!is.null(yInit)) {
model <- "celda_CG"
} else {
model <- "celda_C"
}
celdaList <- .recursiveSplitCellWithSeed(counts = x,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
altExp <- .createSCERecursiveSplitCell(celdaList = celdaList,
sce = SingleCellExperiment::altExp(sce, altExpName),
xClass = xClass,
useAssay = useAssay,
model = model,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
SingleCellExperiment::altExp(sce, altExpName) <- altExp
return(sce)
}
)
.recursiveSplitCellWithSeed <- function(counts,
sampleLabel,
initialK,
maxK,
tempL,
yInit,
alpha,
beta,
delta,
gamma,
minCell,
reorder,
seed,
perplexity,
logfile,
verbose) {
if (is.null(seed)) {
celdaList <- .recursiveSplitCell(counts = counts,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
} else {
with_seed(
seed,
celdaList <- .recursiveSplitCell(counts = counts,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
)
}
return(celdaList)
}
.recursiveSplitCell <- function(counts,
sampleLabel,
initialK,
maxK,
tempL,
yInit,
alpha,
beta,
delta,
gamma,
minCell,
reorder,
perplexity,
logfile,
verbose) {
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = FALSE,
verbose = verbose
)
.logMessages("Starting recursive cell population splitting.",
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.validateCounts(counts)
startTime <- Sys.time()
counts <- .processCounts(counts)
countChecksum <- .createCountChecksum(counts)
sampleLabel <- .processSampleLabels(sampleLabel, numCells = ncol(counts))
s <- as.integer(sampleLabel)
names <- list(
row = rownames(counts),
column = colnames(counts),
sample = levels(sampleLabel)
)
if (!is.null(yInit)) {
# Create collapsed module matrix
L <- length(unique(yInit))
.logMessages(date(),
".. Collapsing to",
L,
"modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
overallY <- .initializeCluster(L, nrow(counts), initial = yInit)
countsY <- .rowSumByGroup(counts, overallY, L)
# Create initial model with initialK and predifined y labels
.logMessages(date(),
".. Initializing with",
initialK,
"populations",
append = TRUE,
verbose = verbose,
logfile = logfile)
modelInitial <- .celda_CG(counts,
sampleLabel = s,
K = as.integer(initialK),
L = as.integer(L),
zInitialize = "split",
yInitialize = "predefined",
nchains = 1,
yInit = overallY,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
verbose = FALSE,
reorder = reorder)
currentK <- length(unique(celdaClusters(modelInitial)$z)) + 1
overallZ <- celdaClusters(modelInitial)$z
resList <- list(modelInitial)
while (currentK <= maxK) {
# previousY <- overallY
tempSplit <- .singleSplitZ(countsY,
overallZ,
s,
currentK,
minCell = 3,
alpha = alpha,
beta = beta
)
tempModel <- .celda_CG(counts,
sampleLabel = s,
K = as.integer(currentK),
L = as.integer(L),
yInit = overallY,
zInit = tempSplit$z,
nchains = 1,
zInitialize = "predefined",
yInitialize = "predefined",
splitOnLast = FALSE,
stopIter = 5,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
verbose = FALSE,
reorder = reorder
)
# Calculate new decomposed counts matrix with new module labels
# overallY = clusters(tempModel)$y
# p = .cGReDecomposeCounts(counts, overallY, previousY, countsY,
# nByG, L = as.integer(L))
# countsY = p$nTSByC
# If the number of clusters is still "currentK", then keep the
# reordering, otherwise keep the previous configuration
if (length(unique(celdaClusters(tempModel)$z)) == currentK) {
overallZ <- celdaClusters(tempModel)$z
} else {
overallZ <- tempSplit$z
ll <- .logLikelihoodcelda_CG(
counts,
s,
overallZ,
celdaClusters(tempModel)$y,
currentK,
L,
alpha,
beta,
delta,
gamma
)
tempModel <- methods::new("celda_CG",
clusters = list(z = overallZ, y = celdaClusters(tempModel)$y),
params = list(
K = as.integer(currentK),
L = as.integer(L),
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
countChecksum = countChecksum
),
finalLogLik = ll,
sampleLabel = sampleLabel,
names = names
)
}
resList <- c(resList, list(tempModel))
.logMessages(date(),
".. Current cell population",
currentK,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = logfile
)
currentK <- length(unique(overallZ)) + 1
}
runK <- vapply(resList, function(mod) {
params(mod)$K
}, integer(1))
runL <- vapply(resList, function(mod) {
params(mod)$L
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
L = as.integer(runL),
K = as.integer(runK),
stringsAsFactors = FALSE
)
} else if (!is.null(tempL)) {
L <- tempL
.logMessages(date(),
".. Collapsing to",
L,
"temporary modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
tempY <- .initializeSplitY(counts,
L = as.integer(L),
tempK = max(100, maxK),
minFeature = 3
)
tempY <- as.integer(as.factor(tempY))
L <- length(unique(tempY)) # Recalculate in case some modules are empty
countsY <- .rowSumByGroup(counts, tempY, L)
# Create initial model with initialK
.logMessages(date(),
".. Initializing with",
initialK,
"populations",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_C(countsY,
sampleLabel = s,
K = as.integer(initialK),
zInitialize = "split",
nchains = 1,
alpha = alpha,
beta = beta,
verbose = FALSE,
reorder = reorder
)
currentK <- length(unique(celdaClusters(modelInitial)$z)) + 1
overallZ <- celdaClusters(modelInitial)$z
ll <- .logLikelihoodcelda_C(
counts, s, overallZ, currentK,
alpha, beta
)
modelInitial@params$countChecksum <- countChecksum
modelInitial@completeLogLik <- ll
modelInitial@finalLogLik <- ll
resList <- list(modelInitial)
while (currentK <= maxK) {
# Find next best split, then do a new celda_C run with that split
tempSplit <- .singleSplitZ(countsY,
overallZ,
s,
currentK,
minCell = 3,
alpha = alpha,
beta = beta
)
tempModel <- .celda_C(countsY,
sampleLabel = s,
K = as.integer(currentK),
nchains = 1,
zInitialize = "random",
alpha = alpha,
beta = beta,
stopIter = 5,
splitOnLast = FALSE,
verbose = FALSE,
zInit = tempSplit$z,
reorder = reorder
)
# Handle rare cases where a population has no cells after running
# the model
if (length(unique(celdaClusters(tempModel)$z)) == currentK) {
overallZ <- celdaClusters(tempModel)$z
} else {
overallZ <- tempSplit$z
}
# Need to change below line to use decompose counts to save time
ll <- .logLikelihoodcelda_C(
counts, s, overallZ, currentK,
alpha, beta
)
tempModel <- methods::new("celda_C",
clusters = list(z = overallZ),
params = list(
K = as.integer(currentK),
alpha = alpha,
beta = beta,
countChecksum = countChecksum
),
finalLogLik = ll,
sampleLabel = sampleLabel,
names = names
)
resList <- c(resList, list(tempModel))
.logMessages(date(),
".. Current cell population",
currentK,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = logfile
)
currentK <- length(unique(overallZ)) + 1
}
runK <- vapply(resList, function(mod) {
params(mod)$K
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
K = as.integer(runK),
stringsAsFactors = FALSE
)
} else {
# Create initial model with initialK
.logMessages(date(),
".. Initializing with",
initialK,
"populations",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_C(counts,
sampleLabel = s,
K = as.integer(initialK),
zInitialize = "split",
nchains = 1,
alpha = alpha,
beta = beta,
verbose = FALSE,
reorder = reorder
)
currentK <- length(unique(celdaClusters(modelInitial)$z)) + 1
overallZ <- celdaClusters(modelInitial)$z
resList <- list(modelInitial)
while (currentK <= maxK) {
tempSplit <- .singleSplitZ(counts,
overallZ,
s,
currentK,
minCell = 3,
alpha = alpha,
beta = beta
)
tempModel <- .celda_C(counts,
sampleLabel = s,
K = as.integer(currentK),
nchains = 1,
zInitialize = "random",
alpha = alpha,
beta = beta,
stopIter = 5,
splitOnLast = FALSE,
verbose = FALSE,
zInit = tempSplit$z,
reorder = reorder
)
if (length(unique(celdaClusters(tempModel)$z)) == currentK) {
overallZ <- celdaClusters(tempModel)$z
} else {
overallZ <- tempSplit$z
ll <-
.logLikelihoodcelda_C(
counts, s, overallZ,
currentK, alpha, beta
)
tempModel <- methods::new("celda_C",
clusters = list(z = overallZ),
params = list(
K = as.integer(currentK),
alpha = alpha,
beta = beta,
countChecksum = countChecksum
),
finalLogLik = ll,
sampleLabel = sampleLabel,
names = names
)
}
resList <- c(resList, list(tempModel))
.logMessages(date(),
".. Current cell population",
currentK,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = logfile
)
currentK <- length(unique(overallZ)) + 1
}
runK <- vapply(resList, function(mod) {
params(mod)$K
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
K = as.integer(runK),
stringsAsFactors = FALSE
)
}
# Summarize paramters of different models
logliks <- vapply(resList, function(mod) {
bestLogLikelihood(mod)
}, double(1))
runParams <- data.frame(runParams,
log_likelihood = logliks,
stringsAsFactors = FALSE
)
celdaRes <- methods::new("celdaList",
runParams = runParams,
resList = resList,
countChecksum = countChecksum
)
if (isTRUE(perplexity)) {
.logMessages(date(),
".. Calculating perplexity",
append = TRUE,
verbose = verbose,
logfile = NULL
)
celdaRes <- resamplePerplexity(counts, celdaRes)
}
endTime <- Sys.time()
.logMessages(
paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(
"Completed recursive cell population splitting. Total time:",
format(difftime(endTime, startTime)),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(
paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
return(celdaRes)
}
#' @title Recursive module splitting
#' @description Uses the \link{celda_G} model to cluster features into modules
#' for a range of possible L's. The module labels of the previous "L-1" model
#' are used as the initial values in the current model with L modules. The best
#' split of an existing module is found to create the L-th module. This
#' procedure is much faster than randomly initializing each model with a
#' different L.
#' @param x A numeric \link{matrix} of counts or a
#' \linkS4class{SingleCellExperiment}
#' with the matrix located in the assay slot under \code{useAssay}.
#' Rows represent features and columns represent cells.
#' @param useAssay A string specifying which \link{assay}
#' slot to use if \code{x} is a
#' \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param initialL Integer. Minimum number of modules to try.
#' @param maxL Integer. Maximum number of modules to try.
#' @param tempK Integer. Number of temporary cell populations to identify and
#' use in module splitting. Only used if \code{zInit = NULL} Collapsing cells
#' to a relatively smaller number of cell popluations will increase the
#' speed of module clustering and tend to produce better modules. This number
#' should be larger than the number of true cell populations expected in the
#' dataset. Default 100.
#' @param zInit Integer vector. Collapse cells to cell populations based on
#' labels in \code{zInit} and then perform module splitting. If NULL, no
#' collapasing will be performed unless \code{tempK} is specified.
#' Default NULL.
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell
#' (column) in the count matrix. Only used if \code{zInit} is set.
#' @param alpha Numeric. Concentration parameter for Theta. Adds a pseudocount
#' to each cell population in each sample. Only used if \code{zInit} is set.
#' Default 1.
#' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount
#' to each feature module in each cell. Default 1.
#' @param delta Numeric. Concentration parameter for Psi. Adds a pseudocount
#' to each feature in each module. Default 1.
#' @param gamma Numeric. Concentration parameter for Eta. Adds a pseudocount
#' to the number of features in each module. Default 1.
#' @param minFeature Integer. Only attempt to split modules with at least this
#' many features.
#' @param reorder Logical. Whether to reorder modules using hierarchical
#' clustering after each model has been created. If FALSE, module numbers will
#' correspond to the split which created the module (i.e. 'L15' was created at
#' split 15, 'L16' was created at split 16, etc.). Default TRUE.
#' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,
#' a default value of 12345 is used. If NULL, no calls to
#' \link[withr]{with_seed} are made.
#' @param perplexity Logical. Whether to calculate perplexity for each model.
#' If FALSE, then perplexity can be calculated later with
#' \link{resamplePerplexity}. Default TRUE.
#' @param verbose Logical. Whether to print log messages. Default TRUE.
#' @param logfile Character. Messages will be redirected to a file named
#' "logfile". If NULL, messages will be printed to stdout. Default NULL.
#' @param ... Ignored. Placeholder to prevent check warning.
#' @return A \linkS4class{SingleCellExperiment} object. Function
#' parameter settings and celda model results are stored in the
#' \link{metadata} \code{"celda_grid_search"} slot. The models in
#' the list will be of class \link{celda_G} if \code{zInit = NULL} or
#' \link{celda_CG} if \code{zInit} is set.
#' @seealso \code{recursiveSplitCell} for recursive splitting of cell
#' populations.
#' @export
setGeneric("recursiveSplitModule", function(x, ...) {
standardGeneric("recursiveSplitModule")})
#' @rdname recursiveSplitModule
#' @examples
#' data(sceCeldaCG)
#' ## Create models that range from L=3 to L=20 by recursively splitting modules
#' ## into two
#' moduleSplit <- recursiveSplitModule(sceCeldaCG, initialL = 3, maxL = 20)
#'
#' ## Example results with perplexity
#' plotGridSearchPerplexity(moduleSplit)
#'
#' ## Select model for downstream analysis
#' celdaMod <- subsetCeldaList(moduleSplit, list(L = 10))
#' @export
setMethod("recursiveSplitModule",
signature(x = "SingleCellExperiment"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
initialL = 10,
maxL = 100,
tempK = 100,
zInit = NULL,
sampleLabel = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minFeature = 3,
reorder = TRUE,
seed = 12345,
perplexity = TRUE,
verbose = TRUE,
logfile = NULL) {
xClass <- "SingleCellExperiment"
if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {
stop(altExpName, " not in 'altExpNames(x)'. Run ",
"selectFeatures(x) first!")
}
altExp <- SingleCellExperiment::altExp(x, altExpName)
if (!useAssay %in% SummarizedExperiment::assayNames(altExp)) {
stop(useAssay, " not in assayNames(altExp(x, altExpName))")
}
counts <- SummarizedExperiment::assay(altExp, i = useAssay)
if (!is.null(zInit)) {
model <- "celda_CG"
} else {
model <- "celda_G"
}
celdaList <- .recursiveSplitModuleWithSeed(counts = counts,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
altExp <- .createSCERecursiveSplitModule(celdaList = celdaList,
sce = altExp,
xClass = xClass,
useAssay = useAssay,
model = model,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
}
)
#' @rdname recursiveSplitModule
#' @examples
#' data(celdaCGSim)
#' ## Create models that range from L=3 to L=20 by recursively splitting modules
#' ## into two
#' moduleSplit <- recursiveSplitModule(celdaCGSim$counts,
#' initialL = 3, maxL = 20)
#'
#' ## Example results with perplexity
#' plotGridSearchPerplexity(moduleSplit)
#'
#' ## Select model for downstream analysis
#' celdaMod <- subsetCeldaList(moduleSplit, list(L = 10))
#' @export
setMethod("recursiveSplitModule",
signature(x = "matrix"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
initialL = 10,
maxL = 100,
tempK = 100,
zInit = NULL,
sampleLabel = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minFeature = 3,
reorder = TRUE,
seed = 12345,
perplexity = TRUE,
verbose = TRUE,
logfile = NULL) {
ls <- list()
ls[[useAssay]] <- x
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)
SingleCellExperiment::altExp(sce, altExpName) <- sce
xClass <- "matrix"
if (!is.null(zInit)) {
model <- "celda_CG"
} else {
model <- "celda_G"
}
celdaList <- .recursiveSplitModuleWithSeed(counts = x,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
altExp <- .createSCERecursiveSplitModule(celdaList = celdaList,
sce = SingleCellExperiment::altExp(sce, altExpName),
xClass = xClass,
useAssay = useAssay,
model = model,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
SingleCellExperiment::altExp(sce, altExpName) <- altExp
return(sce)
}
)
.recursiveSplitModuleWithSeed <- function(counts,
initialL,
maxL,
tempK,
zInit,
sampleLabel,
alpha,
beta,
delta,
gamma,
minFeature,
reorder,
seed,
perplexity,
verbose,
logfile) {
if (is.null(seed)) {
celdaList <- .recursiveSplitModule(
counts = counts,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
} else {
with_seed(seed,
celdaList <- .recursiveSplitModule(
counts = counts,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
sampleLabel = sampleLabel,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
perplexity = perplexity,
verbose = verbose,
logfile = logfile)
)
}
return(celdaList)
}
.recursiveSplitModule <- function(counts,
initialL = 10,
maxL = 100,
tempK = 100,
zInit = NULL,
sampleLabel = NULL,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
minFeature = 3,
reorder = TRUE,
perplexity = TRUE,
verbose = TRUE,
logfile = NULL) {
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = FALSE,
verbose = verbose
)
.logMessages("Starting recursive module splitting.",
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
startTime <- Sys.time()
.validateCounts(counts)
counts <- .processCounts(counts)
countChecksum <- .createCountChecksum(counts)
names <-
list(row = rownames(counts), column = colnames(counts))
sampleLabel <- .processSampleLabels(sampleLabel,
numCells = ncol(counts)
)
s <- as.integer(sampleLabel)
if (!is.null(zInit)) {
# Create collapsed module matrix
K <- length(unique(zInit))
.logMessages(
date(),
".. Collapsing to",
K,
"cell populations",
append = TRUE,
verbose = verbose,
logfile = logfile
)
overallZ <- .initializeCluster(
N = K,
len = ncol(counts),
initial = zInit
)
countsZ <- .colSumByGroup(counts, overallZ, K)
# Create initial model with initialL and predifined z labels
.logMessages(date(),
".. Initializing with",
initialL,
"modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_CG(counts,
sampleLabel = s,
L = initialL,
K = K,
zInitialize = "predefined",
yInitialize = "split",
nchains = 1,
zInit = overallZ,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
verbose = FALSE,
reorder = reorder)
currentL <- length(unique(celdaClusters(modelInitial)$y)) + 1
overallY <- celdaClusters(modelInitial)$y
resList <- list(modelInitial)
while (currentL <= maxL) {
# Allow features to cluster further with celda_CG
tempSplit <- .singleSplitY(
countsZ,
overallY,
currentL,
minFeature = 3,
beta = beta,
delta = delta,
gamma = gamma
)
tempModel <- .celda_CG(
counts,
L = currentL,
K = K,
stopIter = 5,
splitOnIter = -1,
splitOnLast = FALSE,
nchains = 1,
verbose = FALSE,
yInitialize = "predefined",
zInitialize = "predefined",
yInit = tempSplit$y,
zInit = overallZ,
reorder = reorder
)
overallY <- celdaClusters(tempModel)$y
## Add new model to results list and increment L
.logMessages(
date(),
".. Created module",
currentL,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = NULL
)
resList <- c(resList, list(tempModel))
currentL <- currentL + 1
}
runK <- vapply(resList, function(mod) {
params(mod)$K
}, integer(1))
runL <- vapply(resList, function(mod) {
params(mod)$L
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
L = runL,
K = runK,
stringsAsFactors = FALSE
)
} else if (!is.null(tempK)) {
K <- tempK
.logMessages(
date(),
".. Collapsing to",
K,
"temporary cell populations",
append = TRUE,
verbose = verbose,
logfile = logfile
)
z <- .initializeSplitZ(counts,
K = K,
minCell = 3
)
countsZ <- .colSumByGroup(counts, z, length(unique(z)))
.logMessages(
date(),
".. Initializing with",
initialL,
"modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_G(
countsZ,
L = initialL,
nchains = 1,
verbose = FALSE
)
currentL <- length(unique(celdaClusters(modelInitial)$y)) + 1
overallY <- celdaClusters(modelInitial)$y
## Decomposed counts for full count matrix
p <- .cGDecomposeCounts(counts, overallY, currentL)
nTSByC <- p$nTSByC
nByTS <- p$nByTS
nGByTS <- p$nGByTS
nByG <- p$nByG
nG <- p$nG
nM <- p$nM
resList <- list(modelInitial)
while (currentL <= maxL) {
# Allow features to cluster further
previousY <- overallY
tempSplit <- .singleSplitY(
countsZ,
overallY,
currentL,
minFeature = 3,
beta = beta,
delta = delta,
gamma = gamma
)
tempModel <- .celda_G(
countsZ,
L = currentL,
stopIter = 5,
splitOnIter = -1,
splitOnLast = FALSE,
nchains = 1,
verbose = FALSE,
yInitialize = "predefined",
yInit = tempSplit$y,
reorder = reorder
)
overallY <- celdaClusters(tempModel)$y
# Adjust decomposed count matrices
p <- .cGReDecomposeCounts(counts,
overallY,
previousY,
nTSByC,
nByG,
L = currentL
)
nTSByC <- p$nTSByC
nByTS <- p$nByTS
nGByTS <- p$nGByTS
previousY <- overallY
## Create the final model object with correct info on full counts
## matrix
tempModel@finalLogLik <- .cGCalcLL(
nTSByC = nTSByC,
nByTS = nByTS,
nByG = nByG,
nGByTS = nGByTS,
nM = nM,
nG = nG,
L = currentL,
beta = beta,
delta = delta,
gamma = gamma
)
tempModel@completeLogLik <- bestLogLikelihood(tempModel)
tempModel@params$countChecksum <- countChecksum
tempModel@names <- names
## Add extra row/column for next round of L
nTSByC <- rbind(nTSByC, rep(0L, ncol(nTSByC)))
nByTS <- c(nByTS, 0L)
nGByTS <- c(nGByTS, 0L)
## Add new model to results list and increment L
.logMessages(
date(),
".. Created module",
currentL,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = NULL
)
resList <- c(resList, list(tempModel))
currentL <- currentL + 1
}
runL <- vapply(resList, function(mod) {
params(mod)$L
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
L = runL,
stringsAsFactors = FALSE
)
} else {
.logMessages(
date(),
".. Initializing with",
initialL,
"modules",
append = TRUE,
verbose = verbose,
logfile = logfile
)
modelInitial <- .celda_G(
counts,
L = initialL,
maxIter = 20,
nchains = 1,
verbose = FALSE
)
overallY <- celdaClusters(modelInitial)$y
currentL <- length(unique(overallY)) + 1
## Perform splitting for y labels
resList <- list(modelInitial)
while (currentL <= maxL) {
# Allow features to cluster further
previousY <- overallY
tempSplit <- .singleSplitY(
counts,
overallY,
currentL,
minFeature = 3,
beta = beta,
delta = delta,
gamma = gamma
)
tempModel <- .celda_G(
counts,
L = currentL,
stopIter = 5,
splitOnIter = -1,
splitOnLast = FALSE,
nchains = 1,
verbose = FALSE,
yInitialize = "predefined",
yInit = tempSplit$y,
reorder = reorder
)
overallY <- celdaClusters(tempModel)$y
## Add new model to results list and increment L
.logMessages(
date(),
".. Created module",
currentL,
"| logLik:",
bestLogLikelihood(tempModel),
append = TRUE,
verbose = verbose,
logfile = NULL
)
resList <- c(resList, list(tempModel))
currentL <- currentL + 1
}
runL <- vapply(resList, function(mod) {
params(mod)$L
}, integer(1))
runParams <- data.frame(
index = seq.int(1, length(resList)),
L = runL,
stringsAsFactors = FALSE
)
}
## Summarize paramters of different models
logliks <- vapply(resList, function(mod) {
bestLogLikelihood(mod)
}, double(1))
runParams <- data.frame(runParams,
log_likelihood = logliks,
stringsAsFactors = FALSE
)
celdaRes <- methods::new(
"celdaList",
runParams = runParams,
resList = resList,
countChecksum = countChecksum
)
if (isTRUE(perplexity)) {
.logMessages(
date(),
".. Calculating perplexity",
append = TRUE,
verbose = verbose,
logfile = NULL
)
celdaRes <- resamplePerplexity(counts, celdaRes)
}
endTime <- Sys.time()
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages("Completed recursive module splitting. Total time:",
format(difftime(endTime, startTime)),
logfile = logfile,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("=", 50), collapse = ""),
logfile = logfile,
append = TRUE,
verbose = verbose
)
return(celdaRes)
}
.createSCERecursiveSplitCell <- function(celdaList,
sce,
xClass,
useAssay,
model,
sampleLabel,
initialK,
maxK,
tempL,
yInit,
alpha,
beta,
delta,
gamma,
minCell,
reorder,
seed,
perplexity,
logfile,
verbose) {
S4Vectors::metadata(sce)[["celda_grid_search"]] <- celdaList
S4Vectors::metadata(sce)$celda_grid_search@celdaGridSearchParameters <-
list(xClass = xClass,
useAssay = useAssay,
model = model,
sampleLabel = sampleLabel,
initialK = initialK,
maxK = maxK,
tempL = tempL,
yInit = yInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minCell = minCell,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
return(sce)
}
.createSCERecursiveSplitModule <- function(celdaList,
sce,
xClass,
useAssay,
model,
initialL,
maxL,
tempK,
zInit,
sampleLabel,
alpha,
beta,
delta,
gamma,
minFeature,
reorder,
seed,
perplexity,
verbose,
logfile) {
S4Vectors::metadata(sce)[["celda_grid_search"]] <- celdaList
S4Vectors::metadata(sce)$celda_grid_search@celdaGridSearchParameters <-
list(xClass = xClass,
useAssay = useAssay,
model = model,
sampleLabel = sampleLabel,
initialL = initialL,
maxL = maxL,
tempK = tempK,
zInit = zInit,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
minFeature = minFeature,
reorder = reorder,
seed = seed,
perplexity = perplexity,
logfile = logfile,
verbose = verbose)
return(sce)
}
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