R/mca.R

In cbl-imagine/cellID: Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis

#' Run Multiple Correspondence Analysis
#'
#' @param X Seurat, SingleCellExperiment or matrix object
#' @param nmcs number of components to compute and store, default set to 30
#' @param features character vector of feature names. If not specified all features will be taken.
#' @param reduction.name name of the reduction default set to "MCA" for SingleCellExperiment and mca
#' @param slot  Which slot to pull expression data from?
#' @param ... other aruments passed to methods
#'
#' @return Seurat or SCE object with MCA calculation stored in the reductions slot.
#' @importClassesFrom Seurat Seurat
#' @importClassesFrom SingleCellExperiment SingleCellExperiment
#' @importFrom SummarizedExperiment assay
#' @export
#'
#' @examples
#' seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5)
RunMCA <- function(X, nmcs, features, reduction.name, slot, ...) {
    UseMethod("RunMCA", X)
}

#' @rdname RunMCA
#' @export
RunMCA.matrix <-
    function(X, nmcs = 50, features = NULL, reduction.name = "MCA", ...) {
        # preprocessing matrix ----------------------------------------------------
        if (!is.null(features)) {
            X <- X[features,]
        }
        X <- as.matrix(X)
        X <- X[rowVars(X) != 0,]
        X <- X[str_length(rownames(X)) > 0,]
        X <- X[!duplicated(rownames(X)),]
        cellsN <- colnames(X)
        featuresN <- rownames(X)
        tic()
        message("Computing Fuzzy Matrix")
        MCAPrepRes <- MCAStep1(X)
        toc()
        message("Computing SVD")
        tic()
        SVD <- irlba::irlba(A = MCAPrepRes$Z, nv = nmcs + 1,nu = 1)[seq(3)]
        toc()
        message("Computing Coordinates")
        tic()
        MCA <- MCAStep2(Z = MCAPrepRes$Z,V = SVD$v[,-1],Dc = MCAPrepRes$Dc)
        component                         <- paste0(reduction.name, "_" ,seq(ncol(MCA$cellsCoordinates)))
        colnames(MCA$cellsCoordinates)    <- component
        colnames(MCA$featuresCoordinates) <- component
        rownames(MCA$cellsCoordinates)    <- cellsN
        rownames(MCA$featuresCoordinates) <- featuresN
        MCA$stdev <- SVD$d[-1]
        class(MCA) <- "MCA"
        toc()
        return(MCA)
    }

#' @rdname RunMCA
#' @param assay Name of Assay MCA is being run on
#' @export
RunMCA.Seurat <-
    function(X, nmcs = 50, features = NULL, reduction.name = "mca", slot = "data", assay = DefaultAssay(X), ...) {
        data_matrix <- as.matrix(GetAssayData(X, slot))
        MCA <- RunMCA(X = data_matrix, 
                      nmcs = nmcs, 
                      features = features)
        geneEmb <- MCA$featuresCoordinates
        cellEmb <- MCA$cellsCoordinates
        stdev <- MCA$stdev
        X <-
            setDimMCSlot(
                X = X,
                cellEmb = cellEmb,
                geneEmb = geneEmb,
                stdev = stdev,
                reduction.name = reduction.name
            )
        return(X)
    }

#' @rdname RunMCA
#' @export
RunMCA.SingleCellExperiment <-
    function(X, nmcs = 50, features = NULL,  reduction.name = "MCA", slot = "logcounts", ...) {
        data_matrix <- as.matrix(SummarizedExperiment::assay(X, slot))
        MCA <-
            RunMCA(
                X = data_matrix,
                nmcs = nmcs,
                features = NULL,
                reduction.name = reduction.name
            )
        geneEmb <- MCA$featuresCoordinates
        cellEmb <- MCA$cellsCoordinates
        stdev <- MCA$stdev
        X <-
            setDimMCSlot(X,
                cellEmb = cellEmb,
                geneEmb = geneEmb,
                stdev = stdev,
                reduction.name = reduction.name
            )
        return(X)
    }

# SetDimSlot --------------------------------------------------------------

#' SetDimSlot
#'
#' Integrate MCA in Seurat and SingleCellExperiment Dimensionlity reduction Slot.
#' It will set also a small parameter inside the dimensionality reduction object to signal if it is a MCA or not.
#'
#' @param X Seurat or SingleCellExperiment object
#' @param cellEmb cell coordinates returned by MCA
#' @param geneEmb feature coordinates returned by MCA
#' @param stdev eigen value returned by MCA
#' @param reduction.name name of the created dimensionlaity reduction, default set to "mca" for Seurat and "MCA" for SCE.
#' @param ... other arguments passed to methods
#'
#' @return Seurat or SingleCellExperiment object with MC stored in the reduction slot
setDimMCSlot <-
    function(X, cellEmb, geneEmb, stdev, reduction.name, ...) {
        UseMethod("setDimMCSlot", X)
    }

#' @rdname setDimMCSlot
#' @param assay Seurat assay slot
setDimMCSlot.Seurat <-
    function(X, cellEmb, geneEmb, stdev = NULL, reduction.name = "mca", assay = DefaultAssay(X), ...) {
        colnames(cellEmb) <- paste0(reduction.name, "_", seq(ncol(cellEmb)))
        colnames(geneEmb) <-
            paste0(reduction.name, "_", seq(ncol(geneEmb)))
        DimReducObject <- CreateDimReducObject(
            embeddings = cellEmb,
            loadings = geneEmb,
            key = paste0(reduction.name, "_"),
            assay = assay
        )
        X@reductions[[reduction.name]] <- DimReducObject
        if (!is.null(stdev)) {
            X@reductions[[reduction.name]]@stdev <- sqrt(stdev)
        }
        X@reductions[[reduction.name]]@misc[["mca.flag"]] <- TRUE
        return(X)
    }

#' @rdname setDimMCSlot
setDimMCSlot.SingleCellExperiment <-
    function(X, cellEmb, geneEmb, stdev = NULL, reduction.name = "MCA", ...) {
        reducedDim(X, reduction.name) <- cellEmb
        attr(reducedDim(X, reduction.name), "genesCoordinates") <-
            geneEmb
        attr(reducedDim(X, reduction.name), "mcaFlag") <- TRUE
        if (!is.null(stdev)) {
            attr(reducedDim(X, reduction.name), "stdev") <- stdev
        }
        return(X)
    }