R/InputData.R

In carter-allen/IRISFGM: Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

#' Read 10X HDF5 file based on Seurat package
#'
#' This function provide a method for reading in HDF5 file from 10X platform.
#'
#' @param input Input an HDF5 object
#' @param use.names Use barcode, default is true
#' @param unique.features  use gene name, default is true
#'
#' @return The output from \code{\link{Read10X_h5}}
#' @export
#' @importFrom Matrix sparseMatrix
#' @return It will return a gene expression matrix. 
#' @examples \dontrun{input_mat <- ReadFrom10X_h5(input= 'my.h5')}
ReadFrom10X_h5 <- function(input = NULL, use.names = TRUE, unique.features = TRUE) {
    if (!requireNamespace("hdf5r", quietly = TRUE)) {
        stop("Please install hdf5r by using install.packages('hdf5r')")
    }
    infile <- hdf5r::H5File$new(filename = input, mode = "r")
    genomes <- names(x = infile)
    output <- list()
    if (!infile$attr_exists("PYTABLES_FORMAT_VERSION")) {
        if (use.names) {
            feature_slot <- "features/name"
        } else {
            feature_slot <- "features/id"
        }
    } else {
        if (use.names) {
            feature_slot <- "gene_names"
        } else {
            feature_slot <- "genes"
        }
    }
    for (genome in genomes) {
        counts <- infile[[paste0(genome, "/data")]]
        indices <- infile[[paste0(genome, "/indices")]]
        indptr <- infile[[paste0(genome, "/indptr")]]
        shp <- infile[[paste0(genome, "/shape")]]
        features <- infile[[paste0(genome, "/", feature_slot)]][]
        barcodes <- infile[[paste0(genome, "/barcodes")]]
        sparse.mat <- sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x = counts[]), dims = shp[], giveCsparse = FALSE)
        if (unique.features) {
            features <- make.unique(names = features)
        }
        rownames(x = sparse.mat) <- features
        colnames(x = sparse.mat) <- barcodes[]
        sparse.mat <- as(object = sparse.mat, Class = "dgCMatrix")
        if (infile$exists(name = paste0(genome, "/features"))) {
            types <- infile[[paste0(genome, "/features/feature_type")]][]
            types.unique <- unique(x = types)
            if (length(x = types.unique) > 1) {
                message("Genome ", genome, " has multiple modalities, returning a list of matrices for this genome")
                sparse.mat <- vapply(X = types.unique, FUN = function(x) {
                    return(sparse.mat[which(x = types == x), ])
                }, simplify = FALSE, USE.NAMES = TRUE)
            }
        }
        output[[genome]] <- sparse.mat
    }
    infile$close_all()
    if (length(x = output) == 1) {
        return(output[[genome]])
    } else {
        return(output)
    }
}

#' @rdname ReadFrom10X_h5
#' @export
setMethod("ReadFrom10X_h5", "IRISFGM", ReadFrom10X_h5)


#' Read 10X folder based on Seurat package
#' 
#' This function provide a method for reading in a folder from 10X platform. In this folder, it should contain three files: barcode, matrix, and gene.
#'
#' @param input.dir Input directory. It should contain three file, including barcode file, feature file, and sparse counts matrix.
#'
#' @return The output from \code{\link{Read10X}}
#' @export
#' @importFrom Matrix readMM
#'
#' @examples \dontrun{input_mat <- ReadFrom10X_folder(input.dir = 'my_path_to_folder')}
ReadFrom10X_folder <- function(input.dir = NULL) {
    
    my.path <- input.dir
    if (!dir.exists(paths = my.path)) {
        stop("Directory provided does not exist")
    }
    tmp.file <- list.files(path = my.path, pattern = "*")
    gene.check <- c(any(grepl("gene", tmp.file)) | any(grepl("feature", tmp.file)))
    barcode.check <- any(grepl("barcode", tmp.file))
    matrix.check <- any(grepl("matrix", tmp.file))
    if (gene.check == FALSE) {
        stop(" cannot find gene name, please check the file with gene name.")
    }
    if (barcode.check == FALSE) {
        stop(" cannot find barcode information, please check the file with barcode.")
    }
    if (matrix.check == FALSE) {
        stop(" cannot find sparse matrix, please check the expression matrix")
    }
    if (any(grepl("gene", tmp.file))) {
        gene.path <- file.path(my.path, tmp.file[grepl("gene", tmp.file)])
    } else if (any(grepl("feature", tmp.file))) {
        gene.path <- file.path(my.path, tmp.file[grepl("feature", tmp.file)])
    }
    barcode.path <- file.path(my.path, tmp.file[grepl("barcode", tmp.file)])
    matrix.path <- file.path(my.path, tmp.file[grepl("matrix", tmp.file)])
    matrix.readin <- readMM(file = matrix.path)
    cellID.readin <- readLines(barcode.path)
    cellID <- gsub("-1$", "", cellID.readin)
    geneID.readin <- read.delim(gene.path, sep = "\t", stringsAsFactors = FALSE, header = FALSE)
    geneID <- make.unique(geneID.readin$V2)
    if (ncol(x = geneID.readin) > 2) {
        data.types <- factor(x = geneID.readin$V3)
        lvls <- levels(x = data.types)
        expr.name <- "Gene Expression"
        if (expr.name %in% lvls) {
            lvls <- c(expr.name, lvls[-which(lvls == expr.name)])
        }
        geneID <- geneID[which(geneID.readin$V3 == lvls)]
        
        
    } else {
        geneID <- geneID
    }
    colnames(matrix.readin) <- cellID
    rownames(matrix.readin) <- geneID
    return(matrix.readin)
}

#' @rdname ReadFrom10X_folder
#' @export
setMethod("ReadFrom10X_folder", "IRISFGM", ReadFrom10X_folder)