| 9f8e453d |
#' @title Cell and feature clustering with Celda
|
| 5a6c5283 |
#' @description Clusters the rows and columns of a count matrix containing
#' single-cell data into L modules and K subpopulations, respectively.
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells.
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell
#' (column) in the count matrix.
|
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#' @param K Integer. Number of cell populations.
#' @param L Integer. Number of feature modules.
|
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#' @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 module in each cell population. 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 algorithm String. Algorithm to use for clustering cell subpopulations.
#' One of 'EM' or 'Gibbs'. The EM algorithm for cell clustering is faster,
#' especially for larger numbers of cells. However, more chains may be required
#' to ensure a good solution is found. Default 'EM'.
#' @param stopIter Integer. Number of iterations without improvement in the log
#' likelihood to stop inference. Default 10.
#' @param maxIter Integer. Maximum number of iterations of Gibbs sampling to
#' perform. Default 200.
#' @param splitOnIter Integer. On every `splitOnIter` iteration, a heuristic
#' will be applied to determine if a cell population or feature module should
#' be reassigned and another cell population or feature module should be split
#' into two clusters. To disable splitting, set to -1. Default 10.
#' @param splitOnLast Integer. After `stopIter` iterations have been
#' performed without improvement, a heuristic will be applied to determine if
#' a cell population or feature module should be reassigned and another cell
#' population or feature module should be split into two clusters. If a split
#' occurs, then 'stopIter' will be reset. Default TRUE.
|
| 7365c4e1 |
#' @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.
|
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#' @param nchains Integer. Number of random cluster initializations. Default 3.
|
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#' @param zInitialize Chararacter. One of 'random', 'split', or 'predefined'.
#' With 'random', cells are randomly assigned to a populations. With 'split',
#' cells will be split into sqrt(K) populations and then each popluation will
#' be subsequently split into another sqrt(K) populations. With 'predefined',
#' values in `zInit` will be used to initialize `z`. Default 'split'.
#' @param yInitialize Chararacter. One of 'random', 'split', or 'predefined'.
#' With 'random', features are randomly assigned to a modules. With 'split',
#' features will be split into sqrt(L) modules and then each module will be
#' subsequently split into another sqrt(L) modules. With 'predefined', values
#' in `yInit` will be used to initialize `y`. Default 'split'.
#' @param zInit Integer vector. Sets initial starting values of z. If NULL,
#' starting values for each cell will be randomly sampled from 1:K. 'zInit'
#' can only be used when `initialize' = 'random'`. Default NULL.
#' @param yInit Integer vector. Sets initial starting values of y. If NULL,
#' starting values for each feature will be randomly sampled from 1:L.
#' 'yInit' can only be used when `initialize = 'random'`. Default NULL.
#' @param countChecksum Character. An MD5 checksum for the `counts` matrix.
#' Default NULL.
#' @param logfile Character. Messages will be redirected to a file named
#' `logfile`. If NULL, messages will be printed to stdout. Default NULL.
|
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#' @param verbose Logical. Whether to print log messages. Default TRUE.
|
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#' @return An object of class `celda_CG` with the cell populations clusters
#' stored in in `z` and feature module clusters stored in `y`.
#' @seealso `celda_G()` for feature clustering and `celda_C()` for clustering
#' cells. `celdaGridSearch()` can be used to run multiple values of K/L and
#' multiple chains in parallel.
|
| ec7b91a6 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim)
|
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#' celdaMod <- celda_CG(celdaCGSim$counts,
#' K = celdaCGSim$K,
#' L = celdaCGSim$L,
#' sampleLabel = celdaCGSim$sampleLabel,
#' nchains = 1)
|
| 3de9437b |
#' @import Rcpp RcppEigen
|
| 2905885c |
#' @rawNamespace import(gridExtra, except = c(combine))
|
| af260337 |
#' @export
|
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celda_CG <- function(counts,
sampleLabel = NULL,
K,
L,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
algorithm = c("EM", "Gibbs"),
stopIter = 10,
maxIter = 200,
splitOnIter = 10,
splitOnLast = TRUE,
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seed = 12345,
|
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nchains = 3,
zInitialize = c("split", "random", "predefined"),
yInitialize = c("split", "random", "predefined"),
countChecksum = NULL,
zInit = NULL,
yInit = NULL,
logfile = NULL,
verbose = TRUE) {
.validateCounts(counts)
|
| c358fce6 |
if (is.null(seed)) {
res <- .celda_CG(
|
| 5a6c5283 |
counts,
sampleLabel,
K,
L,
alpha,
beta,
delta,
gamma,
algorithm,
stopIter,
maxIter,
splitOnIter,
splitOnLast,
nchains,
zInitialize,
yInitialize,
countChecksum,
zInit,
yInit,
logfile,
verbose,
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| c358fce6 |
reorder = TRUE)
} else {
with_seed(seed,
res <- .celda_CG(
counts,
sampleLabel,
K,
L,
alpha,
beta,
delta,
gamma,
algorithm,
stopIter,
maxIter,
splitOnIter,
splitOnLast,
nchains,
zInitialize,
yInitialize,
countChecksum,
zInit,
yInit,
logfile,
verbose,
reorder = TRUE))
}
return(res)
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}
|
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.celda_CG <- function(counts,
sampleLabel = NULL,
K,
L,
alpha = 1,
beta = 1,
delta = 1,
gamma = 1,
algorithm = c("EM", "Gibbs"),
stopIter = 10,
maxIter = 200,
splitOnIter = 10,
splitOnLast = TRUE,
nchains = 3,
zInitialize = c("split", "random", "predefined"),
yInitialize = c("split", "random", "predefined"),
countChecksum = NULL,
zInit = NULL,
yInit = NULL,
logfile = NULL,
verbose = TRUE,
reorder = TRUE) {
|
| d2e8abdb |
.logMessages(paste(rep("-", 50), collapse = ""),
|
| 5a6c5283 |
logfile = logfile,
append = FALSE,
verbose = verbose)
|
| d2e8abdb |
.logMessages("Starting Celda_CG: Clustering cells and genes.",
|
| 5a6c5283 |
logfile = logfile,
append = TRUE,
verbose = verbose)
|
| d2e8abdb |
.logMessages(paste(rep("-", 50), collapse = ""),
|
| 5a6c5283 |
logfile = logfile,
append = TRUE,
verbose = verbose)
startTime <- Sys.time()
counts <- .processCounts(counts)
if (is.null(countChecksum)) {
countChecksum <- .createCountChecksum(counts)
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}
|
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sampleLabel <- .processSampleLabels(sampleLabel, ncol(counts))
s <- as.integer(sampleLabel)
algorithm <- match.arg(algorithm)
algorithmFun <- ifelse(algorithm == "Gibbs",
".cCCalcGibbsProbZ",
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".cCCalcEMProbZ")
|
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zInitialize <- match.arg(zInitialize)
yInitialize <- match.arg(yInitialize)
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allChains <- seq(nchains)
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# Pre-compute lgamma values
lggamma <- lgamma(seq(0, nrow(counts) + L) + gamma)
lgdelta <- c(NA, lgamma((seq(nrow(counts) + L) * delta)))
bestResult <- NULL
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for (i in allChains) {
|
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## Initialize cluster labels
|
| d2e8abdb |
.logMessages(date(),
|
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".. Initializing 'z' in chain",
i,
"with",
|
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paste0("'", zInitialize, "' "),
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logfile = logfile,
append = TRUE,
verbose = verbose)
|
| d2e8abdb |
.logMessages(date(),
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".. Initializing 'y' in chain",
i,
"with",
|
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paste0("'", yInitialize, "' "),
|
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logfile = logfile,
append = TRUE,
verbose = verbose)
if (zInitialize == "predefined") {
if (is.null(zInit)) {
stop("'zInit' needs to specified when initilize.z == 'given'.")
}
|
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z <- .initializeCluster(K,
|
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ncol(counts),
initial = zInit,
|
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fixed = NULL)
|
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} else if (zInitialize == "split") {
|
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z <- .initializeSplitZ(
|
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counts,
K = K,
alpha = alpha,
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beta = beta)
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} else {
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z <- .initializeCluster(K,
|
| 5a6c5283 |
ncol(counts),
initial = NULL,
|
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fixed = NULL)
|
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}
if (yInitialize == "predefined") {
if (is.null(yInit)) {
stop("'yInit' needs to specified when initilize.y == 'given'.")
}
|
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y <- .initializeCluster(L,
|
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nrow(counts),
initial = yInit,
|
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fixed = NULL)
|
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} else if (yInitialize == "split") {
|
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y <- .initializeSplitY(counts,
|
| 5a6c5283 |
L,
beta = beta,
delta = delta,
|
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gamma = gamma)
|
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} else {
|
| 25256e1e |
y <- .initializeCluster(L,
|
| 5a6c5283 |
nrow(counts),
initial = NULL,
|
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fixed = NULL)
|
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}
zBest <- z
yBest <- y
## Calculate counts one time up front
p <- .cCGDecomposeCounts(counts, s, z, y, K, L)
mCPByS <- p$mCPByS
nTSByC <- p$nTSByC
nTSByCP <- p$nTSByCP
nCP <- p$nCP
nByG <- p$nByG
nByC <- p$nByC
nByTS <- p$nByTS
nGByTS <- p$nGByTS
nGByCP <- p$nGByCP
nM <- p$nM
nG <- p$nG
nS <- p$nS
rm(p)
ll <- .cCGCalcLL(K = K,
L = L,
mCPByS = mCPByS,
nTSByCP = nTSByCP,
nByG = nByG,
nByTS = nByTS,
nGByTS = nGByTS,
nS = nS,
nG = nG,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma)
iter <- 1L
numIterWithoutImprovement <- 0L
doCellSplit <- TRUE
doGeneSplit <- TRUE
while (iter <= maxIter & numIterWithoutImprovement <= stopIter) {
## Gibbs sampling for each gene
lgbeta <- lgamma(seq(0, max(nCP)) + beta)
nextY <- .cGCalcGibbsProbY(counts = nGByCP,
nTSByC = nTSByCP,
nByTS = nByTS,
nGByTS = nGByTS,
nByG = nByG,
y = y,
L = L,
nG = nG,
beta = beta,
delta = delta,
gamma = gamma,
lgbeta = lgbeta,
lggamma = lggamma,
lgdelta = lgdelta)
nTSByCP <- nextY$nTSByC
nGByTS <- nextY$nGByTS
nByTS <- nextY$nByTS
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nTSByC <- .rowSumByGroupChange(counts, nTSByC, nextY$y, y, L)
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y <- nextY$y
## Gibbs or EM sampling for each cell
nextZ <- do.call(algorithmFun, list(counts = nTSByC,
mCPByS = mCPByS,
nGByCP = nTSByCP,
nCP = nCP,
nByC = nByC,
z = z,
s = s,
K = K,
nG = L,
nM = nM,
alpha = alpha,
beta = beta))
mCPByS <- nextZ$mCPByS
nTSByCP <- nextZ$nGByCP
nCP <- nextZ$nCP
nGByCP <- .colSumByGroupChange(counts, nGByCP, nextZ$z, z, K)
z <- nextZ$z
## Perform split on i-th iteration defined by splitOnIter
tempLl <- .cCGCalcLL(K = K,
L = L,
mCPByS = mCPByS,
nTSByCP = nTSByCP,
nByG = nByG,
nByTS = nByTS,
nGByTS = nGByTS,
nS = nS,
nG = nG,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma)
if (L > 2 & iter != maxIter &
(((numIterWithoutImprovement == stopIter &
!all(tempLl > ll)) & isTRUE(splitOnLast)) |
(splitOnIter > 0 & iter %% splitOnIter == 0 &
isTRUE(doGeneSplit)))) {
|
| d2e8abdb |
.logMessages(date(),
|
| 5a6c5283 |
" .... Determining if any gene clusters should be split.",
logfile = logfile,
append = TRUE,
sep = "",
verbose = verbose)
res <- .cCGSplitY(counts,
y,
mCPByS,
nGByCP,
nTSByC,
nTSByCP,
nByG,
nByTS,
nGByTS,
nCP,
s,
z,
K,
L,
nS,
nG,
alpha,
beta,
delta,
gamma,
yProb = t(nextY$probs),
maxClustersToTry = max(L / 2, 10),
minCell = 3)
|
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.logMessages(res$message,
|
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logfile = logfile,
append = TRUE,
verbose = verbose)
# Reset convergence counter if a split occured
if (!isTRUE(all.equal(y, res$y))) {
numIterWithoutImprovement <- 1L
doGeneSplit <- TRUE
} else {
doGeneSplit <- FALSE
}
## Re-calculate variables
y <- res$y
nTSByCP <- res$nTSByCP
nByTS <- res$nByTS
nGByTS <- res$nGByTS
nTSByC <- .rowSumByGroup(counts, group = y, L = L)
}
|
| bf9aff71 |
|
| b6cf56ae |
if (K > 2 & iter != maxIter &
|
| 5a6c5283 |
(((numIterWithoutImprovement == stopIter &
!all(tempLl > ll)) & isTRUE(splitOnLast)) |
(splitOnIter > 0 & iter %% splitOnIter == 0 &
isTRUE(doCellSplit)))) {
|
| d2e8abdb |
.logMessages(date(),
|
| 5a6c5283 |
" .... Determining if any cell clusters should be split.",
logfile = logfile,
append = TRUE,
sep = "",
verbose = verbose)
res <- .cCGSplitZ(counts,
mCPByS,
nTSByC,
nTSByCP,
nByG,
nByTS,
nGByTS,
nCP,
s,
z,
K,
L,
nS,
nG,
alpha,
beta,
delta,
gamma,
zProb = t(nextZ$probs),
maxClustersToTry = K,
minCell = 3)
|
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.logMessages(res$message,
|
| 5a6c5283 |
logfile = logfile,
append = TRUE,
verbose = verbose)
# Reset convergence counter if a split occured
if (!isTRUE(all.equal(z, res$z))) {
numIterWithoutImprovement <- 0L
doCellSplit <- TRUE
} else {
doCellSplit <- FALSE
}
## Re-calculate variables
z <- res$z
mCPByS <- res$mCPByS
nTSByCP <- res$nTSByCP
nCP <- res$nCP
nGByCP <- .colSumByGroup(counts, group = z, K = K)
}
## Calculate complete likelihood
tempLl <- .cCGCalcLL(K = K,
L = L,
mCPByS = mCPByS,
nTSByCP = nTSByCP,
nByG = nByG,
nByTS = nByTS,
nGByTS = nGByTS,
nS = nS,
nG = nG,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma)
if ((all(tempLl > ll)) | iter == 1) {
zBest <- z
yBest <- y
llBest <- tempLl
numIterWithoutImprovement <- 1L
} else {
numIterWithoutImprovement <- numIterWithoutImprovement + 1L
}
ll <- c(ll, tempLl)
|
| d2e8abdb |
.logMessages(date(),
|
| 5a6c5283 |
" .... Completed iteration: ",
iter,
" | logLik: ",
tempLl,
logfile = logfile,
append = TRUE,
sep = "",
verbose = verbose)
iter <- iter + 1L
}
names <- list(row = rownames(counts),
column = colnames(counts),
sample = levels(sampleLabel))
result <- list(z = zBest,
y = yBest,
completeLogLik = ll,
finalLogLik = llBest,
K = K,
L = L,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
sampleLabel = sampleLabel,
names = names,
countChecksum = countChecksum)
class(result) <- "celda_CG"
if (is.null(bestResult) ||
result$finalLogLik > bestResult$finalLogLik) {
bestResult <- result
}
|
| d2e8abdb |
.logMessages(date(),
|
| 5a6c5283 |
".. Finished chain",
i,
logfile = logfile,
append = TRUE,
verbose = verbose)
}
|
| af260337 |
|
| 5a6c5283 |
## Peform reordering on final Z and Y assigments:
bestResult <- methods::new("celda_CG",
clusters = list(z = zBest, y = yBest),
|
| af4c3cb8 |
params = list(K = as.integer(K),
L = as.integer(L),
|
| 5a6c5283 |
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
countChecksum = countChecksum),
completeLogLik = ll,
finalLogLik = llBest,
sampleLabel = sampleLabel,
names = names)
if (isTRUE(reorder)) {
bestResult <- .reorderCeldaCG(counts = counts, res = bestResult)
}
|
| af260337 |
|
| 5a6c5283 |
endTime <- Sys.time()
|
| d2e8abdb |
.logMessages(paste(rep("-", 50), collapse = ""),
|
| 5a6c5283 |
logfile = logfile,
append = TRUE,
verbose = verbose)
|
| d2e8abdb |
.logMessages("Completed Celda_CG. Total time:",
|
| 5a6c5283 |
format(difftime(endTime, startTime)),
logfile = logfile,
append = TRUE,
verbose = verbose)
|
| 58380509 |
.logMessages(paste(rep("-", 50), collapse = ""),
|
| 5a6c5283 |
logfile = logfile,
append = TRUE,
verbose = verbose)
return(bestResult)
}
|
| af260337 |
|
| 63a280d7 |
#' @title Simulate cells from the celda_CG model
|
| 5a6c5283 |
#' @description Generates a simulated counts matrix, cell subpopulation
#' clusters, sample labels, and feature module clusters according to the
#' generative process of the celda_CG model.
#' @param model Character. Options available in `celda::availableModels`.
|
| bf9aff71 |
#' @param S Integer. Number of samples to simulate. Default 5.
|
| 5a6c5283 |
#' @param CRange Integer vector. A vector of length 2 that specifies the lower
#' and upper bounds of the number of cells to be generated in each sample.
#' Default c(50, 100).
#' @param NRange Integer vector. A vector of length 2 that specifies the lower
#' and upper bounds of the number of counts generated for each cell. Default
#' c(500, 1000).
|
| 48cd350b |
#' @param G Integer. The total number of features to be simulated. Default 100.
|
| bf9aff71 |
#' @param K Integer. Number of cell populations. Default 5.
|
| 48cd350b |
#' @param L Integer. Number of feature modules. Default 10.
|
| 5a6c5283 |
#' @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 module in each cell population. Default 1.
#' @param gamma Numeric. Concentration parameter for Eta. Adds a pseudocount to
#' the number of features in each module. Default 5.
#' @param delta Numeric. Concentration parameter for Psi. Adds a pseudocount to
#' each feature in each module. Default 1.
|
| 7365c4e1 |
#' @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.
|
| bf9aff71 |
#' @param ... Additional parameters.
|
| 5a6c5283 |
#' @return List. Contains the simulated matrix `counts`, cell population
#' clusters `z`, feature module clusters `y`, sample assignments `sampleLabel`,
#' and input parameters.
#' @seealso `celda_C()` for simulating cell subpopulations and `celda_G()` for
#' simulating feature modules.
|
| 2f6fec9b |
#' @examples
|
| 30fa8113 |
#' celdaCGSim <- simulateCells(model = "celda_CG")
|
| af260337 |
#' @export
|
| 804d499b |
simulateCellscelda_CG <- function(model,
|
| 5a6c5283 |
S = 5,
CRange = c(50, 100),
NRange = c(500, 1000),
G = 100,
K = 5,
L = 10,
alpha = 1,
beta = 1,
gamma = 5,
delta = 1,
|
| c358fce6 |
seed = 12345,
...) {
if (is.null(seed)) {
res <- .simulateCellscelda_CG(model = model,
S = S,
CRange = CRange,
NRange = NRange,
G = G,
K = K,
L = L,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
...)
} else {
with_seed(seed,
res <- .simulateCellscelda_CG(model = model,
S = S,
CRange = CRange,
NRange = NRange,
G = G,
K = K,
L = L,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
...))
}
return(res)
}
.simulateCellscelda_CG <- function(model = model,
S = S,
CRange = CRange,
NRange = NRange,
G = G,
K = K,
L = L,
alpha = alpha,
beta = beta,
gamma = gamma,
delta = delta,
|
| 5a6c5283 |
...) {
## Number of cells per sample
nC <- sample(seq(CRange[1], CRange[2]), size = S, replace = TRUE)
nCSum <- sum(nC)
cellSampleLabel <- rep(seq(S), nC)
## Select number of transcripts per cell
nN <- sample(seq(NRange[1], NRange[2]),
size = length(cellSampleLabel),
replace = TRUE)
## Generate cell population distribution for each sample
theta <- t(.rdirichlet(S, rep(alpha, K)))
## Assign cells to cellular subpopulations
z <- unlist(lapply(seq(S), function(i) {
sample(seq(K),
size = nC[i],
prob = theta[, i],
replace = TRUE)
}))
## Generate transcriptional state distribution for each cell subpopulation
phi <- .rdirichlet(K, rep(beta, L))
## Assign genes to gene modules
eta <- .rdirichlet(1, rep(gamma, L))
y <- sample(seq(L),
size = G,
prob = eta,
replace = TRUE)
if (length(table(y)) < L) {
warning("Some gene modules did not receive any genes after sampling.",
" Try increasing G and/or making gamma larger.")
L <- length(table(y))
y <- as.integer(as.factor(y))
}
psi <- matrix(0, nrow = G, ncol = L)
for (i in seq(L)) {
ind <- y == i
psi[ind, i] <- .rdirichlet(1, rep(delta, sum(ind)))
}
## Select transcript distribution for each cell
cellCounts <- matrix(0, nrow = G, ncol = nCSum)
for (i in seq(nCSum)) {
|
| af4c3cb8 |
transcriptionalStateDist <- as.integer(stats::rmultinom(1,
|
| 5a6c5283 |
size = nN[i], prob = phi[z[i], ]))
for (j in seq(L)) {
if (transcriptionalStateDist[j] > 0) {
cellCounts[, i] <- cellCounts[, i] + stats::rmultinom(1,
size = transcriptionalStateDist[j], prob = psi[, j])
}
}
}
## Ensure that there are no all-0 rows in the counts matrix, which violates
## a celda modeling
## constraint (columns are guarnteed at least one count):
zeroRowIdx <- which(rowSums(cellCounts) == 0)
if (length(zeroRowIdx > 0)) {
cellCounts <- cellCounts[-zeroRowIdx, ]
y <- y[-zeroRowIdx]
|
| bf9aff71 |
}
|
| 5a6c5283 |
## Assign gene/cell/sample names
rownames(cellCounts) <- paste0("Gene_", seq(nrow(cellCounts)))
colnames(cellCounts) <- paste0("Cell_", seq(ncol(cellCounts)))
cellSampleLabel <- paste0("Sample_", seq(S))[cellSampleLabel]
cellSampleLabel <- factor(cellSampleLabel,
levels = paste0("Sample_", seq(S)))
## Peform reordering on final Z and Y assigments:
cellCounts <- .processCounts(cellCounts)
names <- list(row = rownames(cellCounts),
column = colnames(cellCounts),
sample = unique(cellSampleLabel))
countChecksum <- .createCountChecksum(cellCounts)
result <- methods::new("celda_CG",
clusters = list(z = z, y = y),
|
| af4c3cb8 |
params = list(K = as.integer(K),
L = as.integer(L),
|
| 5a6c5283 |
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma,
countChecksum = countChecksum),
sampleLabel = cellSampleLabel,
names = names
)
result <- .reorderCeldaCG(counts = cellCounts, res = result)
|
| 06b0c870 |
return(list(z = clusters(result)$z,
y = clusters(result)$y,
|
| 5a6c5283 |
sampleLabel = cellSampleLabel,
counts = cellCounts,
K = K,
L = L,
CRange = CRange,
NRange = NRange,
S = S,
alpha = alpha,
beta = beta,
gamma = gamma,
|
| 75664a2f |
delta = delta)
|
| 5a6c5283 |
)
|
| af260337 |
}
|
| 367fa0a7 |
#' @title Matrix factorization for results from celda_CG
|
| 5a6c5283 |
#' @description Generates factorized matrices showing the contribution of each
#' feature in each module, each module in each cell and/or cell population,
#' and each cell population in each sample.
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells. This matrix should be the same as the one used to generate
#' `celdaMod`.
#' @param celdaMod Celda model. Options are "celda_C" or "celda_CG". Celda
#' object of class "celda_CG".
#' @param type Character vector. A vector containing one or more of "counts",
#' "proportion", or "posterior". "counts" returns the raw number of counts for
#' each factorized matrix. "proportions" returns the normalized probabilities
#' for each factorized matrix, which are calculated by dividing the raw counts
#' in each factorized matrix by the total counts in each column. "posterior"
#' returns the posterior estimates. Default
#' `c("counts", "proportion", "posterior")`.
#' @return A list with elements for `counts`, `proportions`, or `posterior`
#' probabilities. Each element will be a list containing factorized matrices
#' for `module`, `cellPopulation`, and `sample`. Additionally, the
#' contribution of each module in each individual cell will be included in the
#' `cell` element of `counts` and `proportions` elements.
|
| 367fa0a7 |
#' @seealso `celda_CG()` for clustering features and cells
|
| bf9aff71 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim, celdaCGMod)
|
| 5a6c5283 |
#' factorizedMatrices <- factorizeMatrix(celdaCGSim$counts,
#' celdaCGMod, "posterior")
|
| bf9aff71 |
#' @export
|
| 5a6c5283 |
setMethod("factorizeMatrix", signature(celdaMod = "celda_CG"),
function(counts,
celdaMod,
type = c("counts", "proportion", "posterior")) {
counts <- .processCounts(counts)
compareCountMatrix(counts, celdaMod)
|
| 06b0c870 |
K <- params(celdaMod)$K
L <- params(celdaMod)$L
z <- clusters(celdaMod)$z
y <- clusters(celdaMod)$y
alpha <- params(celdaMod)$alpha
beta <- params(celdaMod)$beta
delta <- params(celdaMod)$delta
gamma <- params(celdaMod)$gamma
sampleLabel <- sampleLabel(celdaMod)
|
| 5a6c5283 |
s <- as.integer(sampleLabel)
## Calculate counts one time up front
p <- .cCGDecomposeCounts(counts, s, z, y, K, L)
nS <- p$nS
nG <- p$nG
nM <- p$nM
mCPByS <- p$mCPByS
nTSByC <- p$nTSByC
nTSByCP <- p$nTSByCP
nByG <- p$nByG
nByTS <- p$nByTS
nGByTS <- p$nGByTS
nGByTS[nGByTS == 0] <- 1
nGByTS <- matrix(0, nrow = length(y), ncol = L)
nGByTS[cbind(seq(nG), y)] <- p$nByG
LNames <- paste0("L", seq(L))
KNames <- paste0("K", seq(K))
|
| 06b0c870 |
colnames(nTSByC) <- matrixNames(celdaMod)$column
|
| 5a6c5283 |
rownames(nTSByC) <- LNames
colnames(nGByTS) <- LNames
|
| 06b0c870 |
rownames(nGByTS) <- matrixNames(celdaMod)$row
|
| 5a6c5283 |
rownames(mCPByS) <- KNames
|
| 06b0c870 |
colnames(mCPByS) <- matrixNames(celdaMod)$sample
|
| 5a6c5283 |
colnames(nTSByCP) <- KNames
rownames(nTSByCP) <- LNames
countsList <- c()
propList <- c()
postList <- c()
res <- list()
if (any("counts" %in% type)) {
countsList <- list(sample = mCPByS,
cellPopulation = nTSByCP,
cell = nTSByC,
module = nGByTS,
geneDistribution = nGByTS)
res <- c(res, list(counts = countsList))
}
if (any("proportion" %in% type)) {
## Need to avoid normalizing cell/gene states with zero cells/genes
uniqueZ <- sort(unique(z))
tempNTSByCP <- nTSByCP
tempNTSByCP[, uniqueZ] <- normalizeCounts(tempNTSByCP[, uniqueZ],
normalize = "proportion")
uniqueY <- sort(unique(y))
tempNGByTS <- nGByTS
tempNGByTS[, uniqueY] <- normalizeCounts(tempNGByTS[, uniqueY],
normalize = "proportion")
tempNGByTS <- nGByTS / sum(nGByTS)
propList <- list(sample = normalizeCounts(mCPByS,
normalize = "proportion"),
cellPopulation = tempNTSByCP,
cell = normalizeCounts(nTSByC, normalize = "proportion"),
module = tempNGByTS,
geneDistribution = tempNGByTS)
res <- c(res, list(proportions = propList))
}
if (any("posterior" %in% type)) {
gs <- nGByTS
gs[cbind(seq(nG), y)] <- gs[cbind(seq(nG), y)] + delta
gs <- normalizeCounts(gs, normalize = "proportion")
tempNGByTS <- (nGByTS + gamma) / sum(nGByTS + gamma)
postList <- list(sample = normalizeCounts(mCPByS + alpha,
normalize = "proportion"),
cellPopulation = normalizeCounts(nTSByCP + beta,
normalize = "proportion"),
module = gs,
geneDistribution = tempNGByTS)
res <- c(res, posterior = list(postList))
}
return(res)
})
|
| af260337 |
# Calculate the loglikelihood for the celda_CG model
|
| 5a6c5283 |
.cCGCalcLL <- function(K,
L,
mCPByS,
nTSByCP,
nByG,
nByTS,
nGByTS,
nS,
nG,
alpha,
beta,
delta,
gamma) {
nG <- sum(nGByTS)
## Calculate for "Theta" component
a <- nS * lgamma(K * alpha)
b <- sum(lgamma(mCPByS + alpha))
c <- -nS * K * lgamma(alpha)
d <- -sum(lgamma(colSums(mCPByS + alpha)))
thetaLl <- a + b + c + d
## Calculate for "Phi" component
a <- K * lgamma(L * beta)
b <- sum(lgamma(nTSByCP + beta))
c <- -K * L * lgamma(beta)
d <- -sum(lgamma(colSums(nTSByCP + beta)))
phiLl <- a + b + c + d
## Calculate for "Psi" component
a <- sum(lgamma(nGByTS * delta))
b <- sum(lgamma(nByG + delta))
c <- -nG * lgamma(delta)
d <- -sum(lgamma(nByTS + (nGByTS * delta)))
psiLl <- a + b + c + d
## Calculate for "Eta" side
a <- lgamma(L * gamma)
b <- sum(lgamma(nGByTS + gamma))
c <- -L * lgamma(gamma)
d <- -lgamma(sum(nGByTS + gamma))
etaLl <- a + b + c + d
|
| 2e877ffe |
final <- thetaLl + phiLl + psiLl + etaLl
|
| 5a6c5283 |
return(final)
|
| af260337 |
}
|
| a82d1665 |
#' @title Calculate Celda_CG log likelihood
|
| 5a6c5283 |
#' @description Calculates the log likelihood for user-provided cell population
#' and feature module clusters using the `celda_CG()` model.
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells.
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell
#' (column) in the count matrix.
|
| bf9aff71 |
#' @param z Numeric vector. Denotes cell population labels.
#' @param y Numeric vector. Denotes feature module labels.
#' @param K Integer. Number of cell populations.
#' @param L Integer. Number of feature modules.
|
| 5a6c5283 |
#' @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 module in each cell population. 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.
|
| a82d1665 |
#' @return The log likelihood for the given cluster assignments
#' @seealso `celda_CG()` for clustering features and cells
|
| 6839068a |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim)
|
| 804d499b |
#' loglik <- logLikelihoodcelda_CG(celdaCGSim$counts,
|
| 5a6c5283 |
#' sampleLabel = celdaCGSim$sampleLabel,
#' z = celdaCGSim$z,
#' y = celdaCGSim$y,
#' K = celdaCGSim$K,
#' L = celdaCGSim$L,
#' alpha = celdaCGSim$alpha,
#' beta = celdaCGSim$beta,
#' gamma = celdaCGSim$gamma,
#' delta = celdaCGSim$delta)
|
| bf9aff71 |
#'
|
| 5a6c5283 |
#' loglik <- logLikelihood(celdaCGSim$counts,
#' model = "celda_CG",
#' sampleLabel = celdaCGSim$sampleLabel,
#' z = celdaCGSim$z,
#' y = celdaCGSim$y,
#' K = celdaCGSim$K,
#' L = celdaCGSim$L,
#' alpha = celdaCGSim$alpha,
#' beta = celdaCGSim$beta,
#' gamma = celdaCGSim$gamma,
#' delta = celdaCGSim$delta)
|
| af260337 |
#' @export
|
| 804d499b |
logLikelihoodcelda_CG <- function(counts,
|
| 5a6c5283 |
sampleLabel,
z,
y,
K,
L,
alpha,
beta,
delta,
gamma) {
if (sum(z > K) > 0) {
stop("An entry in z contains a value greater than the provided K.")
}
if (sum(y > L) > 0) {
stop("An entry in y contains a value greater than the provided L.")
}
sampleLabel <- .processSampleLabels(sampleLabel, ncol(counts))
s <- as.integer(sampleLabel)
p <- .cCGDecomposeCounts(counts, s, z, y, K, L)
final <- .cCGCalcLL(K = K,
L = L,
mCPByS = p$mCPByS,
nTSByCP = p$nTSByCP,
nByG = p$nByG,
nByTS = p$nByTS,
nGByTS = p$nGByTS,
nS = p$nS,
nG = p$nG,
alpha = alpha,
beta = beta,
delta = delta,
gamma = gamma)
return(final)
|
| af260337 |
}
|
| 5a6c5283 |
# Takes raw counts matrix and converts it to a series of matrices needed for
# log likelihood calculation
# @param counts Integer matrix. Rows represent features and columns represent
# cells.
# @param s Integer vector. Contains the sample label for each cell (column) in
# the count matrix.
|
| bf9aff71 |
# @param z Numeric vector. Denotes cell population labels.
# @param y Numeric vector. Denotes feature module labels.
# @param K Integer. Number of cell populations.
# @param L Integer. Number of feature modules.
|
| 5a6c5283 |
.cCGDecomposeCounts <- function(counts, s, z, y, K, L) {
nS <- length(unique(s))
mCPByS <- matrix(as.integer(table(factor(z, levels = seq(K)), s)),
ncol = nS)
nTSByC <- .rowSumByGroup(counts, group = y, L = L)
nTSByCP <- .colSumByGroup(nTSByC, group = z, K = K)
nCP <- as.integer(colSums(nTSByCP))
nByG <- as.integer(rowSums(counts))
nByC <- as.integer(colSums(counts))
nByTS <- as.integer(.rowSumByGroup(matrix(nByG, ncol = 1),
group = y, L = L))
nGByTS <- tabulate(y, L) + 1 ## Add pseudogene to each module
nGByCP <- .colSumByGroup(counts, group = z, K = K)
nG <- nrow(counts)
nM <- ncol(counts)
return(list(mCPByS = mCPByS,
nTSByC = nTSByC,
nTSByCP = nTSByCP,
nCP = nCP,
nByG = nByG,
nByC = nByC,
nByTS = nByTS,
nGByTS = nGByTS,
nGByCP = nGByCP,
nM = nM,
nG = nG,
nS = nS))
|
| bf9aff71 |
}
|
| af260337 |
|
| 5a6c5283 |
#' @title Conditional probabilities for cells and features from a Celda_CG
#' model
#' @description Calculates the conditional probability of each cell belonging
#' to each subpopulation given all other cell cluster assignments as well as
#' each feature belonging to each module given all other feature cluster
#' assignments in a `celda_CG()` result.
#' @param celdaMod Celda object of class `celda_CG`.
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells. This matrix should be the same as the one used to generate
#' `celdaMod`.
#' @param log Logical. If FALSE, then the normalized conditional probabilities
#' will be returned. If TRUE, then the unnormalized log probabilities will be
#' returned. Default FALSE.
|
| af260337 |
#' @param ... Additional parameters.
|
| 5a6c5283 |
#' @return A list containging a matrix for the conditional cell and feature
#' cluster probabilities.
|
| a82d1665 |
#' @seealso `celda_CG()` for clustering features and cells
|
| 24363d24 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim, celdaCGMod)
|
| 5a6c5283 |
#' clusterProb <- clusterProbability(celdaCGSim$counts, celdaCGMod)
|
| af260337 |
#' @export
|
| 5a6c5283 |
setMethod("clusterProbability", signature(celdaMod = "celda_CG"),
function(counts, celdaMod, log = FALSE, ...) {
|
| 06b0c870 |
s <- as.integer(sampleLabel(celdaMod))
z <- clusters(celdaMod)$z
K <- params(celdaMod)$K
y <- clusters(celdaMod)$y
L <- params(celdaMod)$L
alpha <- params(celdaMod)$alpha
delta <- params(celdaMod)$delta
beta <- params(celdaMod)$beta
gamma <- params(celdaMod)$gamma
|
| 5a6c5283 |
p <- .cCGDecomposeCounts(counts, s, z, y, K, L)
lgbeta <- lgamma(seq(0, max(p$nCP)) + beta)
lggamma <- lgamma(seq(0, nrow(counts) + L) + gamma)
lgdelta <- c(NA, lgamma((seq(nrow(counts) + L) * delta)))
nextZ <- .cCCalcGibbsProbZ(counts = p$nTSByC,
mCPByS = p$mCPByS,
nGByCP = p$nTSByCP,
nCP = p$nCP,
nByC = p$nByC,
z = z,
s = s,
K = K,
nG = L,
nM = p$nM,
alpha = alpha,
beta = beta,
doSample = FALSE)
zProb <- t(nextZ$probs)
## Gibbs sampling for each gene
nextY <- .cGCalcGibbsProbY(counts = p$nGByCP,
nTSByC = p$nTSByCP,
nByTS = p$nByTS,
nGByTS = p$nGByTS,
nByG = p$nByG,
y = y,
L = L,
nG = p$nG,
lgbeta = lgbeta,
lgdelta = lgdelta,
lggamma = lggamma,
delta = delta,
doSample = FALSE)
yProb <- t(nextY$probs)
if (!isTRUE(log)) {
|
| 2e877ffe |
zProb <- .normalizeLogProbs(zProb)
yProb <- .normalizeLogProbs(yProb)
|
| 5a6c5283 |
}
return(list(zProbability = zProb, yProbability = yProb))
})
|
| af260337 |
|
| 91de8c6d |
#' @title Calculate the perplexity on new data with a celda_CG model
|
| 5a6c5283 |
#' @description Perplexity is a statistical measure of how well a probability
#' model can predict new data. Lower perplexity indicates a better model.
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells. This matrix should be the same as the one used to generate
#' `celdaMod`.
#' @param celdaMod Celda object of class "celda_C", "celda_G" or "celda_CG".
#' @param newCounts A new counts matrix used to calculate perplexity. If NULL,
#' perplexity will be calculated for the 'counts' matrix. Default NULL.
|
| 91f4ba11 |
#' @return Numeric. The perplexity for the provided count data and model.
|
| 91de8c6d |
#' @seealso `celda_CG()` for clustering features and cells
|
| 91f4ba11 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim, celdaCGMod)
|
| 5a6c5283 |
#' perplexity <- perplexity(celdaCGSim$counts, celdaCGMod)
|
| d7196f24 |
#' @importFrom matrixStats logSumExp
|
| af260337 |
#' @export
|
| 5a6c5283 |
setMethod("perplexity", signature(celdaMod = "celda_CG"),
function(counts, celdaMod, newCounts = NULL) {
if (!("celda_CG" %in% class(celdaMod))) {
stop("The celdaMod provided was not of class celda_CG.")
}
counts <- .processCounts(counts)
compareCountMatrix(counts, celdaMod)
if (is.null(newCounts)) {
newCounts <- counts
} else {
newCounts <- .processCounts(newCounts)
}
if (nrow(newCounts) != nrow(counts)) {
stop("newCounts should have the same number of rows as counts.")
}
factorized <- factorizeMatrix(counts = counts,
celdaMod = celdaMod,
type = c("posterior", "counts"))
theta <- log(factorized$posterior$sample)
phi <- factorized$posterior$cellPopulation
psi <- factorized$posterior$module
|
| 06b0c870 |
s <- as.integer(sampleLabel(celdaMod))
|
| 5a6c5283 |
eta <- factorized$posterior$geneDistribution
nGByTS <- factorized$counts$geneDistribution
etaProb <- log(eta) * nGByTS
geneByPopProb <- log(psi %*% phi)
innerLogProb <- eigenMatMultInt(geneByPopProb, newCounts) + theta[, s]
# innerLogProb = (t(geneByPopProb) %*% newCounts) + theta[, s]
log.px <- sum(apply(innerLogProb, 2, matrixStats::logSumExp))
# + sum(etaProb)
|
| b6cf56ae |
perplexity <- exp(- (log.px / sum(newCounts)))
|
| 5a6c5283 |
return(perplexity)
})
.reorderCeldaCG <- function(counts, res) {
# Reorder K
|
| 06b0c870 |
if (params(res)$K > 2 & isTRUE(length(unique(clusters(res)$z)) > 1)) {
|
| 5a6c5283 |
|
| 1eaf423b |
res@clusters$z <- as.integer(as.factor(clusters(res)$z))
|
| 5a6c5283 |
fm <- factorizeMatrix(counts = counts,
celdaMod = res,
type = "posterior")
|
| 06b0c870 |
uniqueZ <- sort(unique(clusters(res)$z))
|
| 5a6c5283 |
d <- .cosineDist(fm$posterior$cellPopulation[, uniqueZ])
h <- stats::hclust(d, method = "complete")
res <- recodeClusterZ(res,
from = h$order,
to = seq(length(h$order)))
}
|
| bf9aff71 |
|
| 5a6c5283 |
# Reorder L
|
| 06b0c870 |
if (params(res)$L > 2 & isTRUE(length(unique(clusters(res)$y)) > 1)) {
|
| bf9aff71 |
|
| 53beedc9 |
res@clusters$y <- as.integer(as.factor(clusters(res)$y))
|
| 5a6c5283 |
fm <- factorizeMatrix(counts = counts,
celdaMod = res,
type = "posterior")
|
| 06b0c870 |
uniqueY <- sort(unique(clusters(res)$y))
|
| 5a6c5283 |
cs <- prop.table(t(fm$posterior$cellPopulation[uniqueY, ]), 2)
d <- .cosineDist(cs)
h <- stats::hclust(d, method = "complete")
|
| bf9aff71 |
|
| 5a6c5283 |
res <- recodeClusterY(res, from = h$order, to = seq(length(h$order)))
}
return(res)
|
| af260337 |
}
|
| 5533bb39 |
#' @title Heatmap for celda_CG
|
| 5a6c5283 |
#' @description Renders an expression heatmap to visualize `celda_CG()` results.
#' The top `nfeatures` for each module will be included in the heatmap.
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells. This matrix should be the same as the one used to generate.
#' `celdaMod`.
#' @param celdaMod Celda object of class `celda_CG`.
#' @param nfeatures Integer. Maximum number of features to select for each
#' module. Default 25.
|
| af260337 |
#' @param ... Additional parameters.
|
| 5a6c5283 |
#' @seealso `celda_CG()` for clustering features and cells and `celdaTsne()`
#' for generating 2-dimensional coordinates.
|
| bf9aff71 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim, celdaCGMod)
|
| 5a6c5283 |
#' celdaHeatmap(celdaCGSim$counts, celdaCGMod)
|
| 5533bb39 |
#' @return A list containing dendrograms and the heatmap grob
|
| af260337 |
#' @export
|
| 5a6c5283 |
setMethod("celdaHeatmap", signature(celdaMod = "celda_CG"),
function(counts, celdaMod, nfeatures = 25, ...) {
fm <- factorizeMatrix(counts, celdaMod, type = "proportion")
top <- celda::topRank(fm$proportions$module, n = nfeatures)
ix <- unlist(top$index)
norm <- normalizeCounts(counts,
normalize = "proportion",
transformationFun = sqrt)
plotHeatmap(norm[ix, ],
|
| 06b0c870 |
z = clusters(celdaMod)$z,
y = clusters(celdaMod)$y[ix],
|
| 5a6c5283 |
...)
})
|
| af260337 |
|
| 2ced6125 |
#' @title tSNE for celda_CG
|
| 5a6c5283 |
#' @description Embeds cells in two dimensions using tSNE based on a `celda_CG`
#' model. tSNE is run on module probabilities to reduce the number of features
#' instead of using PCA. Module probabilities square-root trasformed before
#' applying tSNE.
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells. This matrix should be the same as the one used to generate
#' `celdaMod`.
#' @param celdaMod Celda object of class `celda_CG`.
#' @param maxCells Integer. Maximum number of cells to plot. Cells will be
#' randomly subsampled if ncol(counts) > maxCells. Larger numbers of cells
#' requires more memory. Default 25000.
#' @param minClusterSize Integer. Do not subsample cell clusters below this
#' threshold. Default 100.
#' @param initialDims Integer. PCA will be used to reduce the dimentionality
#' of the dataset. The top 'initialDims' principal components will be used
#' for tSNE. Default 20.
#' @param modules Integer vector. Determines which features modules to use for
#' tSNE. If NULL, all modules will be used. Default NULL.
|
| 3df37a6d |
#' @param perplexity Numeric. Perplexity parameter for tSNE. Default 20.
|
| 5a6c5283 |
#' @param maxIter Integer. Maximum number of iterations in tSNE generation.
#' Default 2500.
|
| 7365c4e1 |
#' @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.
|
| 5a6c5283 |
#' @seealso `celda_CG()` for clustering features and cells and `celdaHeatmap()`
#' for displaying expression
|
| 3855c560 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim, celdaCGMod)
|
| 2e877ffe |
#' tsneRes <- celdaTsne(celdaCGSim$counts, celdaCGMod)
|
| 0bd3cd14 |
#' @return A two column matrix of t-SNE coordinates
|
| af260337 |
#' @export
|
| 5a6c5283 |
setMethod("celdaTsne", signature(celdaMod = "celda_CG"),
function(counts,
celdaMod,
maxCells = 25000,
minClusterSize = 100,
initialDims = 20,
modules = NULL,
perplexity = 20,
|
| c358fce6 |
maxIter = 2500,
seed = 12345) {
if (is.null(seed)) {
res <- .celdaTsneCG(counts = counts,
celdaMod = celdaMod,
maxCells = maxCells,
minClusterSize = minClusterSize,
initialDims = initialDims,
modules = modules,
perplexity = perplexity,
maxIter = maxIter)
} else {
with_seed(seed,
res <- .celdaTsneCG(counts = counts,
celdaMod = celdaMod,
maxCells = maxCells,
minClusterSize = minClusterSize,
initialDims = initialDims,
modules = modules,
perplexity = perplexity,
maxIter = maxIter))
}
|
| 5a6c5283 |
|
| c358fce6 |
return(res)
|
| 5a6c5283 |
})
|
| ef11fcec |
|
| c358fce6 |
.celdaTsneCG <- function(counts,
celdaMod,
maxCells = 25000,
minClusterSize = 100,
initialDims = 20,
modules = NULL,
perplexity = 20,
maxIter = 2500) {
preparedCountInfo <- .prepareCountsForDimReductionCeldaCG(counts,
celdaMod,
maxCells,
minClusterSize,
modules)
norm <- preparedCountInfo$norm
res <- .calculateTsne(norm,
doPca = FALSE,
perplexity = perplexity,
maxIter = maxIter,
initialDims = initialDims)
final <- matrix(NA, nrow = ncol(counts), ncol = 2)
final[preparedCountInfo$cellIx, ] <- res
rownames(final) <- colnames(counts)
colnames(final) <- c("tsne_1", "tsne_2")
return(final)
}
|
| 8b60a355 |
#' @title umap for celda_CG
|
| 5a6c5283 |
#' @description Embeds cells in two dimensions using umap based on a `celda_CG`
#' model. umap is run on module probabilities to reduce the number of features
#' instead of using PCA. Module probabilities square-root trasformed before
#' applying tSNE.
|
| bf9aff71 |
#'
|
| 5a6c5283 |
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells. This matrix should be the same as the one used to generate
#' `celdaMod`.
#' @param celdaMod Celda object of class `celda_CG`.
#' @param maxCells Integer. Maximum number of cells to plot. Cells will be
#' randomly subsampled if ncol(counts) > maxCells. Larger numbers of cells
#' requires more memory. Default 25000.
#' @param minClusterSize Integer. Do not subsample cell clusters below this
#' threshold. Default 100.
#' @param modules Integer vector. Determines which features modules to use for
#' tSNE. If NULL, all modules will be used. Default NULL.
|
| 7365c4e1 |
#' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,
#' a default value of 12345 is used. If NULL, no calls to
#' \link[withr]{with_seed} are made.
|
| 5a6c5283 |
#' @param umapConfig Object of class `umap.config`. Configures parameters for
#' umap. Default `umap::umap.defaults`.
#' @seealso `celda_CG()` for clustering features and cells and `celdaHeatmap()`
#' for displaying expression.
|
| 8b60a355 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim, celdaCGMod)
|
| 5a6c5283 |
#' umapRes <- celdaUmap(celdaCGSim$counts, celdaCGMod)
|
| 6e069679 |
#' @return A two column matrix of umap coordinates
|
| 8b60a355 |
#' @export
setMethod("celdaUmap",
|
| 5a6c5283 |
signature(celdaMod = "celda_CG"), function(counts,
celdaMod,
maxCells = 25000,
minClusterSize = 100,
modules = NULL,
|
| c358fce6 |
seed = 12345,
|
| 5a6c5283 |
umapConfig = umap::umap.defaults) {
|
| c358fce6 |
if (is.null(seed)) {
res <- .celdaUmapCG(counts = counts,
celdaMod = celdaMod,
maxCells = maxCells,
minClusterSize = minClusterSize,
modules = modules,
umapConfig = umapConfig)
} else {
with_seed(seed,
res <- .celdaUmapCG(counts = counts,
celdaMod = celdaMod,
maxCells = maxCells,
minClusterSize = minClusterSize,
modules = modules,
umapConfig = umapConfig))
}
return(res)
|
| 5a6c5283 |
})
|
| c358fce6 |
.celdaUmapCG <- function(counts,
celdaMod,
maxCells = 25000,
minClusterSize = 100,
modules = NULL,
umapConfig = umap::umap.defaults) {
preparedCountInfo <- .prepareCountsForDimReductionCeldaCG(counts,
celdaMod,
maxCells,
minClusterSize,
modules)
umapRes <- .calculateUmap(preparedCountInfo$norm, umapConfig)
final <- matrix(NA, nrow = ncol(counts), ncol = 2)
final[preparedCountInfo$cellIx, ] <- umapRes
rownames(final) <- colnames(counts)
colnames(final) <- c("umap_1", "umap_2")
return(final)
}
|
| 5a6c5283 |
.prepareCountsForDimReductionCeldaCG <- function(counts,
celdaMod,
maxCells = 25000,
minClusterSize = 100,
|
| 2e877ffe |
modules = NULL) {
|
| 5a6c5283 |
## Checking if maxCells and minClusterSize will work
if ((maxCells < ncol(counts)) &
|
| 06b0c870 |
(maxCells / minClusterSize < params(celdaMod)$K)) {
|
| 5a6c5283 |
stop("Cannot distribute ",
maxCells,
" cells among ",
|
| 06b0c870 |
params(celdaMod)$K,
|
| 5a6c5283 |
" clusters while maintaining a minumum of ",
minClusterSize,
" cells per cluster. Try increasing 'maxCells' or",
" decreasing 'minClusterSize'.")
|
| 8b60a355 |
}
|
| bf9aff71 |
|
| 5a6c5283 |
fm <- factorizeMatrix(counts = counts,
celdaMod = celdaMod,
type = "counts")
modulesToUse <- seq(nrow(fm$counts$cell))
|
| 8b60a355 |
if (!is.null(modules)) {
|
| 5a6c5283 |
if (!all(modules %in% modulesToUse)) {
stop("'modules' must be a vector of numbers between 1 and ",
modulesToUse,
".")
}
modulesToUse <- modules
|
| 8b60a355 |
}
|
| bf9aff71 |
|
| 5a6c5283 |
## Select a subset of cells to sample if greater than 'maxCells'
totalCellsToRemove <- ncol(counts) - maxCells
zInclude <- rep(TRUE, ncol(counts))
if (totalCellsToRemove > 0) {
|
| 06b0c870 |
zTa <- tabulate(clusters(celdaMod)$z, params(celdaMod)$K)
|
| 5a6c5283 |
## Number of cells that can be sampled from each cluster without
## going below the minimum threshold
clusterCellsToSample <- zTa - minClusterSize
clusterCellsToSample[clusterCellsToSample < 0] <- 0
## Number of cells to sample after exluding smaller clusters
## Rounding can cause number to be off by a few, so ceiling is used
## with a second round of subtraction
clusterNToSample <- ceiling((clusterCellsToSample /
sum(clusterCellsToSample)) * totalCellsToRemove)
diff <- sum(clusterNToSample) - totalCellsToRemove
clusterNToSample[which.max(clusterNToSample)] <-
clusterNToSample[which.max(clusterNToSample)] - diff
## Perform sampling for each cluster
for (i in which(clusterNToSample > 0)) {
|
| 06b0c870 |
zInclude[sample(which(clusters(celdaMod)$z == i),
|
| 5a6c5283 |
clusterNToSample[i])] <- FALSE
}
|
| bf9aff71 |
}
|
| 5a6c5283 |
cellIx <- which(zInclude)
|
| bf9aff71 |
|
| 5a6c5283 |
norm <- t(normalizeCounts(fm$counts$cell[modulesToUse, cellIx],
normalize = "proportion",
transformationFun = sqrt))
return(list(norm = norm, cellIx = cellIx))
|
| 8b60a355 |
}
|
| ef11fcec |
|
| 2ced6125 |
#' @title Probability map for a celda_CG model
|
| 5a6c5283 |
#' @description Renders probability and relative expression heatmaps to
#' visualize the relationship between features and cell populations or cell
#' populations and samples.
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells. This matrix should be the same as the one used to generate
#' `celdaMod`.
#' @param celdaMod Celda object of class `celda_CG`.
#' @param level Character. One of 'cellPopulation' or 'sample'.
#' 'cellPopulation' will display the absolute probabilities and relative
#' normalized expression of each module in each cell population. 'sample'
#' will display the absolute probabilities and relative normalized abundance
#' of each cell population in each sample. Default 'cellPopulation'.
|
| 3af3bb76 |
#' @param ... Additional parameters.
|
| c1a794b4 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim, celdaCGMod)
|
| 5a6c5283 |
#' celdaProbabilityMap(celdaCGSim$counts, celdaCGMod)
|
| 0bd3cd14 |
#' @return A grob containing the specified plots
|
| d7196f24 |
#' @importFrom gridExtra grid.arrange
#' @importFrom RColorBrewer brewer.pal
#' @importFrom grDevices colorRampPalette
|
| 91de8c6d |
#' @seealso `celda_CG()` for clustering features and cells
|
| bf9aff71 |
#' @export
|
| 5a6c5283 |
setMethod("celdaProbabilityMap", signature(celdaMod = "celda_CG"),
function(counts, celdaMod, level = c("cellPopulation", "sample"), ...) {
counts <- .processCounts(counts)
compareCountMatrix(counts, celdaMod)
level <- match.arg(level)
factorized <- factorizeMatrix(celdaMod = celdaMod, counts = counts)
|
| 85379044 |
zInclude <- which(tabulate(clusters(celdaMod)$z,
params(celdaMod)$K) > 0)
yInclude <- which(tabulate(clusters(celdaMod)$y,
params(celdaMod)$L) > 0)
|
| 5a6c5283 |
if (level == "cellPopulation") {
pop <- factorized$proportions$cellPopulation[yInclude,
zInclude, drop = FALSE]
popNorm <- normalizeCounts(pop,
normalize = "proportion",
transformationFun = sqrt,
scaleFun = base::scale)
percentile9 <- round(stats::quantile(pop, .9), digits = 2) * 100
col1 <- grDevices::colorRampPalette(c("#FFFFFF",
RColorBrewer::brewer.pal(n = 9, name = "Blues")))(percentile9)
col2 <- grDevices::colorRampPalette(c("#08306B",
c("#006D2C", "Yellowgreen", "Yellow", "Orange",
"Red")))(100 - percentile9)
col <- c(col1, col2)
breaks <- seq(0, 1, length.out = length(col))
g1 <- plotHeatmap(pop,
colorScheme = "sequential",
scaleRow = NULL,
clusterCell = FALSE,
clusterFeature = FALSE,
showNamesCell = TRUE,
showNamesFeature = TRUE,
breaks = breaks,
col = col,
main = "Absolute Probability",
silent = TRUE
)
g2 <- plotHeatmap(popNorm,
colorScheme = "divergent",
clusterCell = FALSE,
clusterFeature = FALSE,
showNamesCell = TRUE,
showNamesFeature = TRUE,
main = "Relative Expression",
silent = TRUE)
gridExtra::grid.arrange(g1$gtable, g2$gtable, ncol = 2)
} else {
samp <- factorized$proportions$sample
col <- grDevices::colorRampPalette(c("white",
"blue",
"#08306B",
"#006D2C",
"yellowgreen",
"yellow",
"orange",
"red"))(100)
breaks <- seq(0, 1, length.out = length(col))
g1 <- plotHeatmap(samp,
colorScheme = "sequential",
scaleRow = NULL,
clusterCell = FALSE,
clusterFeature = FALSE,
showNamesCell = TRUE,
showNamesFeature = TRUE,
breaks = breaks,
col = col,
main = "Absolute Probability",
silent = TRUE)
if (ncol(samp) > 1) {
sampNorm <- normalizeCounts(factorized$counts$sample,
normalize = "proportion",
transformationFun = sqrt,
scaleFun = base::scale)
g2 <- plotHeatmap(sampNorm,
colorScheme = "divergent",
clusterCell = FALSE,
clusterFeature = FALSE,
showNamesCell = TRUE,
showNamesFeature = TRUE,
main = "Relative Abundance",
silent = TRUE)
gridExtra::grid.arrange(g1$gtable, g2$gtable, ncol = 2)
|
| 5a8d8ecc |
} else {
gridExtra::grid.arrange(g1$gtable)
}
|
| 5a6c5283 |
}
})
|
| ef11fcec |
|
| 91de8c6d |
#' @title Lookup the module of a feature
|
| 5a6c5283 |
#' @description Finds the module assignments of given features in a `celda_G()`
#' model
#' @param counts Integer matrix. Rows represent features and columns represent
#' cells. This matrix should be the same as the one used to generate
#' `celdaMod`.
#' @param celdaMod Model of class `celda_CG`.
#' @param feature Character vector. The module assignemnts will be found for
#' feature names in this vector.
#' @param exactMatch Logical. Whether an exact match or a partial match using
#' `grep()` is used to look up the feature in the rownames of the counts
#' matrix. Default TRUE.
|
| 2ced6125 |
#' @return List. Each element contains the module of the provided feature.
|
| 91de8c6d |
#' @seealso `celda_CG()` for clustering features and cells
|
| 27448271 |
#' @examples
|
| a49fff03 |
#' data(celdaCGSim, celdaCGMod)
|
| 5a6c5283 |
#' module <- featureModuleLookup(celdaCGSim$counts,
#' celdaCGMod,
#' c("Gene_1", "Gene_XXX"))
|
| 9e57de61 |
#' @export
|
| 5a6c5283 |
setMethod("featureModuleLookup", signature(celdaMod = "celda_CG"),
function(counts, celdaMod, feature, exactMatch = TRUE) {
list <- list()
if (!isTRUE(exactMatch)) {
featureGrep <- c()
for (x in seq(length(feature))) {
featureGrep <- c(featureGrep, rownames(counts)[grep(feature[x],
rownames(counts))])
|
| 5a8d8ecc |
}
|
| 5a6c5283 |
feature <- featureGrep
}
for (x in seq(length(feature))) {
if (feature[x] %in% rownames(counts)) {
|
| 06b0c870 |
list[x] <- clusters(celdaMod)$y[which(rownames(counts) ==
|
| 5a6c5283 |
feature[x])]
} else {
list[x] <- paste0("No feature was identified matching '",
feature[x],
"'.")
|
| bf9aff71 |
}
|
| 5a6c5283 |
}
names(list) <- feature
return(list)
})
|
