mixOmics: Omics Data Integration Project

Documented in mint.splsda

# ========================================================================================================
# mint.splsda: perform a vertical sPLS-DA on a combination of experiments, input as a matrix in X
# this function is a particular setting of internal_mint.block,
# the formatting of the input is checked in internal_wrapper.mint, which then call 'internal_mint.block'
# ========================================================================================================

#' P-integration with Discriminant Analysis and variable selection
#' 
#' Function to combine multiple independent studies measured on the same
#' variables or predictors (P-integration) using variants of multi-group sparse
#' PLS-DA for supervised classification with variable selection.
#' 
#' \code{mint.splsda} function fits a vertical sparse PLS-DA models with
#' \code{ncomp} components in which several independent studies measured on the
#' same variables are integrated. The aim is to classify the discrete outcome
#' \code{Y} and select variables that explain the outcome. The \code{study}
#' factor indicates the membership of each sample in each study. We advise to
#' only combine studies with more than 3 samples as the function performs
#' internal scaling per study, and where all outcome categories are
#' represented.
#' 
#' \code{X} can contain missing values. Missing values are handled by being
#' disregarded during the cross product computations in the algorithm
#' \code{mint.splsda} without having to delete rows with missing data.
#' Alternatively, missing data can be imputed prior using the
#' \code{\link{impute.nipals}} function.
#' 
#' The type of deflation used is \code{'regression'} for discriminant algorithms.
#' i.e. no deflation is performed on Y.
#' 
#' Variable selection is performed on each component for \code{X} via input
#' parameter \code{keepX}.
#' 
#' Useful graphical outputs are available, e.g. \code{\link{plotIndiv}},
#' \code{\link{plotLoadings}}, \code{\link{plotVar}}.
#'
#' @inheritParams mint.plsda 
#' @inheritParams mint.spls
#' @template arg/verbose.call
#' @return \code{mint.splsda} returns an object of class \code{"mint.splsda",
#' "splsda"}, a list that contains the following components:
#' 
#' \item{X}{the centered and standardized original predictor matrix.}
#' \item{Y}{the centered and standardized original response vector or matrix.}
#' \item{ind.mat}{the centered and standardized original response vector or
#' matrix.} \item{ncomp}{the number of components included in the model.}
#' \item{study}{The study grouping factor} \item{mode}{the algorithm used to
#' fit the model.} \item{keepX}{Number of variables used to build each
#' component of X} \item{variates}{list containing the variates of X - global
#' variates.} \item{loadings}{list containing the estimated loadings for the
#' variates - global loadings.} \item{variates.partial}{list containing the
#' variates of X relative to each study - partial variates.}
#' \item{loadings.partial}{list containing the estimated loadings for the
#' partial variates - partial loadings.} \item{names}{list containing the names
#' to be used for individuals and variables.} \item{nzv}{list containing the
#' zero- or near-zero predictors information.} \item{iter}{Number of iterations
#' of the algorithm for each component} \item{prop_expl_var}{Percentage of
#' explained variance for each component and each study (note that contrary to
#' PCA, this amount may not decrease as the aim of the method is not to
#' maximise the variance, but the covariance between X and the dummy matrix
#' Y).}
#' \item{call}{if \code{verbose.call = FALSE}, then just the function call is returned.
#' If \code{verbose.call = TRUE} then all the inputted values are accessable via
#' this component}
#' @author Florian Rohart, Kim-Anh Lê Cao, Al J Abadi
#' @seealso \code{\link{spls}}, \code{\link{summary}}, \code{\link{plotIndiv}},
#' \code{\link{plotVar}}, \code{\link{predict}}, \code{\link{perf}},
#' \code{\link{mint.pls}}, \code{\link{mint.plsda}}, \code{\link{mint.plsda}}
#' and http://www.mixOmics.org/mixMINT for more details.
#' @references Rohart F, Eslami A, Matigian, N, Bougeard S, Lê Cao K-A (2017).
#' MINT: A multivariate integrative approach to identify a reproducible
#' biomarker signature across multiple experiments and platforms. BMC
#' Bioinformatics 18:128.
#' 
#' Eslami, A., Qannari, E. M., Kohler, A., and Bougeard, S. (2014). Algorithms
#' for multi-group PLS. J. Chemometrics, 28(3), 192-201.
#' 
#' mixOmics article:
#' 
#' Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics
#' feature selection and multiple data integration. PLoS Comput Biol 13(11):
#' e1005752
#' @keywords regression multivariate
#' @export
#' @examples
#' 
#' data(stemcells)
#' 
#' # -- feature selection
#' res = mint.splsda(X = stemcells$gene, Y = stemcells$celltype, ncomp = 3, keepX = c(10, 5, 15),
#' study = stemcells$study)
#' 
#' plotIndiv(res)
#' #plot study-specific outputs for all studies
#' plotIndiv(res, study = "all.partial")
#' 
#' \dontrun{
#' #plot study-specific outputs for study "2"
#' plotIndiv(res, study = "2")
#' 
#' #plot study-specific outputs for study "2", "3" and "4"
#' plotIndiv(res, study = c(2, 3, 4))
#' }
mint.splsda <- function(X,
                        Y,
                        ncomp = 2,
                        study,
                        keepX = rep(ncol(X), ncomp),
                        scale = TRUE,
                        tol = 1e-06,
                        max.iter = 100,
                        near.zero.var = FALSE,
                        all.outputs = TRUE,
                        verbose.call = FALSE)
{
    
    #-- validation des arguments --#
    # most of the checks are done in 'internal_wrapper.mint'
    if (is.null(Y))
        stop("'Y' has to be something else than NULL.")
    
    if (is.null(dim(Y)))
    {
        Y = factor(Y)
    }  else {
        stop("'Y' should be a factor or a class vector.")
    }
    Y.mat = unmap(Y)
    colnames(Y.mat) = levels(Y)
    
    X = as.matrix(X)
    
    if (length(study) != nrow(X))
        stop(paste0("'study' must be a factor of length ", nrow(X), "."))
    
    if (sum(apply(table(Y, study) != 0, 2, sum) == 1) > 0)
        stop(
            "At least one study only contains a single level of the multi-levels outcome Y. The MINT algorithm cannot be computed."
        )
    
    if (sum(apply(table(Y, study) == 0, 2, sum) > 0) > 0)
        warning(
            "At least one study does not contain all the levels of the outcome Y. The MINT algorithm might not perform as expected."
        )
    
    # call to 'internal_wrapper.mint'
    result <- internal_wrapper.mint(
        X = X,
        Y = Y.mat,
        ncomp = ncomp,
        near.zero.var = near.zero.var,
        study = study,
        mode = 'regression',
        keepX = keepX,
        max.iter = max.iter,
        tol = tol,
        scale = scale,
        all.outputs = all.outputs,
        DA = TRUE
    )
    
    # choose the desired output from 'result'
    out <- list(
        call = match.call(),
        X = result$A[-result$indY][[1]],
        Y = Y,
        ind.mat = result$A[result$indY][[1]],
        ncomp = result$ncomp,
        study = result$study,
        mode = result$mode,
        keepX = result$keepX,
        keepY = result$keepY,
        variates = result$variates,
        loadings = result$loadings,
        variates.partial = result$variates.partial,
        loadings.partial = result$loadings.partial,
        names  =  result$names,
        tol = result$tol,
        iter = result$iter,
        max.iter = result$max.iter,
        nzv = result$nzv,
        scale = result$scale,
        prop_expl_var = result$prop_expl_var
    )
    
    if (verbose.call) {
        c <- out$call
        out$call <- mget(names(formals()))
        out$call <- append(c, out$call)
        names(out$call)[1] <- "simple.call"
    }
    
    class(out) <- c("mint.splsda", "mixo_splsda", "mixo_spls", "DA")
    return(invisible(out))
    
}