R/mint.pca.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

# ========================================================================================================
# mint.pca: perform a vertical PCA 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 Principal Component Analysis
#' 
#' Function to integrate and combine multiple independent studies measured on
#' the same variables or predictors (P-integration) using a multigroup
#' Principal Component Analysis.
#' 
#' \code{mint.pca} fits a vertical PCA model with \code{ncomp} components in
#' which several independent studies measured on the same variables are
#' integrated.  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.
#' 
#' Missing values are handled by being disregarded during the cross product
#' computations in the algorithm without having to delete rows with missing
#' data. Alternatively, missing data can be imputed prior using the
#' \code{nipals} function.
#' 
#' Useful graphical outputs are available, e.g. \code{\link{plotIndiv}},
#' \code{\link{plotLoadings}}, \code{\link{plotVar}}.
#' 
#' @param X numeric matrix of predictors combining multiple independent studies
#' on the same set of predictors. \code{NA}s are allowed.
#' @param ncomp Number of components to include in the model (see Details).
#' Default to 2
#' @param study factor indicating the membership of each sample to each of the
#' studies being combined
#' @param scale Logical. If scale = TRUE, each block is standardized to zero
#' means and unit variances. Default = \code{TRUE}.
#' @param tol Convergence stopping value.
#' @param max.iter integer, the maximum number of iterations.
#' @template arg/verbose.call
#' @return \code{mint.pca} returns an object of class \code{"mint.pca", "pca"},
#' a list that contains the following components:
#' 
#' \item{X}{the centered and standardized original predictor matrix.}
#' \item{ncomp}{the number of components included in the model.}
#' \item{study}{The study grouping factor} \item{sdev}{the eigenvalues of the
#' covariance/correlation matrix, though the calculation is actually done with
#' the singular values of the data matrix or by using NIPALS.} \item{center,
#' scale}{the centering and scaling used, or \code{FALSE}.} \item{rotation}{the
#' matrix of variable loadings (i.e., a matrix whose columns contain the
#' eigenvectors).} \item{loadings}{same as 'rotation' to keep the mixOmics
#' spirit} \item{x}{the value of the rotated data (the centred (and scaled if
#' requested) data multiplied by the rotation/loadings matrix), also called the
#' principal components.} \item{variates}{same as 'x' to keep the mixOmics
#' spirit} \item{prop_expl_var}{Proportion of the explained variance from the multivariate
#' model after setting possible missing values to zero in the data.} \item{names}{list containing the names to be used
#' for individuals and variables.}
#' \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)
#' 
#' res = mint.pca(X = stemcells$gene, ncomp = 3,
#' study = stemcells$study)
#' 
#' plotIndiv(res, group = stemcells$celltype, legend=TRUE)
#' 
mint.pca <- function(X,
                     ncomp = 2,
                     study,
                     scale = TRUE,
                     tol = 1e-06,
                     max.iter = 100,
                     verbose.call = FALSE)
{
    
    #-- checking general input parameters --------------------------------------#
    #---------------------------------------------------------------------------#
    
    #-- check that the user did not enter extra arguments
    arg.call = match.call()
    user.arg = names(arg.call)[-1]
    
    err = tryCatch(mget(names(formals()), sys.frame(sys.nframe())),
                   error = function(e) e)
    
    if ("simpleError" %in% class(err))
        stop(err[[1]], ".", call. = FALSE)
    
    #-- X matrix
    if (is.data.frame(X))
        X = as.matrix(X)
    
    if (!is.matrix(X) || is.character(X))
        stop("'X' must be a numeric matrix.", call. = FALSE)
    
    if (any(apply(X, 1, is.infinite)))
        stop("infinite values in 'X'.", call. = FALSE)
    
    #-- put a names on the rows and columns of X --#
    X.names = colnames(X)
    if (is.null(X.names))
        X.names = paste("V", 1:ncol(X), sep = "")
    
    ind.names = rownames(X)
    if (is.null(ind.names))
        ind.names = 1:nrow(X)
    
    #-- ncomp
    if (is.null(ncomp))
        ncomp = min(nrow(X), ncol(X))
    
    ncomp = round(ncomp)
    
    if (!is.numeric(ncomp) || ncomp < 1 || !is.finite(ncomp))
        stop("invalid value for 'ncomp'.", call. = FALSE)
    
    if (ncomp > min(ncol(X), nrow(X)))
        stop("use smaller 'ncomp'", call. = FALSE)
    
    
    #-- cheking scale
    if (!is.logical(scale))
    {
        if (!is.numeric(scale) || (length(scale) != ncol(X)))
            stop(
                "'scale' should be either a logical value or a numeric vector of length equal to the number of columns of 'X'.",
                call. = FALSE
            )
    }
    
    #-- max.iter
    if (is.null(max.iter) ||
        !is.numeric(max.iter) || max.iter < 1 || !is.finite(max.iter))
        stop("invalid value for 'max.iter'.", call. = FALSE)
    
    max.iter = round(max.iter)
    
    #-- tol
    if (is.null(tol) ||
        !is.numeric(tol) || tol < 0 || !is.finite(tol))
        stop("invalid value for 'tol'.", call. = FALSE)
    
    #set the default study factor
    if (missing(study))
    {
        study = factor(rep(1, nrow(X)))
    } else {
        study = factor(study)
    }
    if (length(study) != nrow(X))
        stop(paste0("'study' must be a factor of length ", nrow(X), "."))
    
    if (any(table(study) <= 1))
        stop(
            "At least one study has only one sample, please consider removing before calling the function again"
        )
    if (any(table(study) < 5))
        warning("At least one study has less than 5 samples, mean centering might not do as expected")
    
    #-- end checking --#
    #------------------#
    
    mean_centered <- mean_centering_per_study(data = X, study = study, scale = scale)
    X_mean_centered <- as.matrix(mean_centered$concat.data)
    
    out = pca(X_mean_centered, ncomp = ncomp, max.iter = max.iter, tol = tol, scale = FALSE)
    
    # choose the desired output from 'result'
    out$study <- study
    
    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.pca","pca")
    return(invisible(out))
    
    
}