R/mint.pls.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

# ========================================================================================================
# mint.pls: perform a vertical PLS 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
#' 
#' Function to integrate and combine multiple independent studies measured on
#' the same variables or predictors (P-integration) using variants of
#' multi-group PLS (unsupervised analysis).
#' 
#' \code{mint.pls} fits a vertical PLS-DA models with \code{ncomp} components
#' in which several independent studies measured on the same variables are
#' integrated. The aim is to explain the continuous outcome \code{Y}. 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.
#' 
#' Multi (continuous)response are supported. \code{X} and \code{Y} can contain
#' missing values. Missing values are handled by being disregarded during the
#' cross product computations in the algorithm \code{mint.pls} without having
#' to delete rows with missing data. Alternatively, missing data can be imputed
#' prior using the \code{nipals} function.
#' 
#' The type of algorithm to use is specified with the \code{mode} argument.
#' Four PLS algorithms are available: PLS regression \code{("regression")}, PLS
#' canonical analysis \code{("canonical")}, redundancy analysis
#' \code{("invariant")} and the classical PLS algorithm \code{("classic")} (see
#' References and more details in \code{?pls}).
#' 
#' Useful graphical outputs are available, e.g. \code{\link{plotIndiv}},
#' \code{\link{plotLoadings}}, \code{\link{plotVar}}.
#' 
#' @inheritParams pls
#' @param X numeric matrix of predictors combining multiple independent studies
#' on the same set of predictors. \code{NA}s are allowed.
#' @param Y Matrix or vector response for a multivariate regression framework.
#' Data should be continuous variables (see \code{mint.plsda} for supervised
#' classification and factor response)
#' @param study Factor, indicating the membership of each sample to each of the
#' studies being combined
#' @template arg/verbose.call
#' @return \code{mint.pls} returns an object of class \code{"mint.pls", "pls"},
#' 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{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{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 data sets).}
#' \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.spls}}, \code{\link{mint.plsda}}, \code{\link{mint.splsda}}
#' 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.
#' @keywords regression multivariate
#' @export
#' @examples
#' 
#' data(stemcells)
#' 
#' # for the purpose of this example, we artificially
#' # create a continuous response Y by taking gene 1.
#' 
#' res = mint.pls(X = stemcells$gene[,-1], Y = stemcells$gene[,1], ncomp = 3,
#' 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", col = 1:3, legend = TRUE)
#' }
mint.pls <- function(X,
                     Y,
                     ncomp = 2,
                     mode = c("regression", "canonical", "invariant", "classic"),
                     study,
                     scale = TRUE,
                     tol = 1e-06,
                     max.iter = 100,
                     near.zero.var = FALSE,
                     all.outputs = TRUE,
                     verbose.call = FALSE)
{
    
    # call to 'internal_wrapper.mint'
    result = internal_wrapper.mint(
        X = X,
        Y = Y,
        ncomp = ncomp,
        scale = scale,
        near.zero.var = near.zero.var,
        study = study,
        mode = mode,
        max.iter = max.iter,
        tol = tol,
        all.outputs = all.outputs,
        DA = FALSE
    )
    
    # choose the desired output from 'result'
    out = list(
        call = match.call(),
        X = result$A[-result$indY][[1]],
        Y = result$A[result$indY][[1]],
        ncomp = result$ncomp,
        study = result$study,
        mode = result$mode,
        variates = result$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.pls","mixo_pls")
    return(invisible(out))
    
    
}