R/Add_meta_data.R

In HailinWei98/SCREEN: What the Package Does (One Line, Title Case)

#' function definitions ##### Add perturbations, sgRNA_num and
#' percent.mt of each cells to the Seurat object.
#' For other downstream function of SCREEN, this step is always needed
#' @export

Add_meta_data <- function(sg_dir, mtx_dir, cal.mt = TRUE, species = "Hs", replicate = 1){
    
    #read files
    
    if (is.character(mtx_dir)) {
        message(paste("Reading RDS file:", mtx_dir))
        mtx <- readRDS(mtx_dir)
    } else {
        mtx <- mtx_dir
    }
    if (is.character(sg_dir)) {
        message(paste("Reading sgRNA lib file:", sg_dir))
        sg_lib <- read.table(sg_dir, header = T)
    } else {
        sg_lib <- sg_dir
    }

    #remove cells in sgRNA library that are not included in matrix
    
    sg_lib_filtered <- subset(sg_lib, cell %in% intersect(sg_lib$cell, colnames(mtx)))

    #label each cells
    
    lab <- rep("blank", times = ncol(mtx))
    sg_num <- rep(0, times = ncol(mtx))
    names(lab) <- colnames(mtx)
    names(sg_num) <- colnames(mtx)
    sg_in_cell <- data.frame(plyr::count(sg_lib_filtered$cell))

    #find unique label and multiple label
    
    for(i in 1:nrow(sg_in_cell)){
        x <- sg_in_cell[i, ]
        if(x[, 2] == 1){
            lab[x[, 1]] <- sg_lib_filtered[which(sg_lib_filtered$cell == x[, 1]), ]$gene}else{
            lab[x[, 1]] <- "multiple"}
    }

    for(i in 1:nrow(sg_in_cell)){
        if(sg_in_cell[i, 1] %in% names(sg_num)){
            sg_num[sg_in_cell[i, 1]] <- sg_in_cell[i, 2]
        }
    }
        
    #add the label information to Seurat object
    
    lab <- as.factor(lab)
    mtx <- AddMetaData(mtx, lab, col.name = "perturbations")
    mtx <- AddMetaData(mtx, sg_num, col.name = "sgRNA_num")

    #Add replicate information to Seurat object
    
    if (!("replicate" %in% colnames(mtx@meta.data))) {
        if(replicate != 1){
            if(is.character(replicate)){
                replicate <- read.table(replicate, header = F)
                replicate <- as.vector(replicate[, 1])
            }
            if(is.vector(replicate) == FALSE){
                stop("Replicate information must be a vector.")
            } else {
                if(is.null(names(replicate))){
                    names(replicate) <- colnames(mtx)
                }
            }
        }
        mtx <- AddMetaData(mtx, as.factor(replicate), col.name = "replicate")
    }

    
    #calculate percent.mt
    
    if(cal.mt == TRUE){
        if(species == "Hs"){
            mtx[["percent.mt"]] <- PercentageFeatureSet(mtx, pattern = "^MT-")
        }else{
            mtx[["percent.mt"]] <- PercentageFeatureSet(mtx, pattern = "^mt-")
        }
    } else {
        if (!("percent.mt" %in% colnames(mtx@meta.data))) {
            message("No 'percent.mt' in meta.data and 'cal.mt == FALSE', set all 'percnet.mt' to 0")
            mtx[["percent.mt"]] <- 0
        }
    }
    
    return(mtx)
}