R/FileIO.R

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

#' Reads in a list of signature input files.
#' @param filenames a list of paths to signature input files
#' @return List of Signature Objects
readSignaturesInput <- function(filenames) {

    # Create a dictionary to easily compute signature sign
    keys <- c("none" = 1.0,  "up" = 1.0, "plus" = 1.0, "down" = -1.0,
            "dn" = -1.0, "minus" = -1.0, "mius" = -1.0)


    # Create a list to store all signatures
    sig_data <- list()

    for (filename in filenames) {
        message("Loading data from ", filename, " ...")

        if (!file.exists(filename)) {
            stop(paste0("Cannot find file: ", filename))
        }

        conn <- file(filename, open = "r")
        lines <- readLines(conn, warn = FALSE)
        close(conn)

        lines <- trimws(lines)
        lines <- strsplit(lines, "\t")

        # Remove invalid lines
        lines <- lines[vapply(lines,
                              function(x) length(x) >= 3, TRUE)]

        for (line in lines) {

            genes <- c()
            values <- c()

            sig <- line[1]
            description <- line[2]
            gene_fields <- line[3:length(line)]

            sig_parts <- unlist(strsplit(sig, "_"))
            key <- tolower(sig_parts[[length(sig_parts)]])

            if (is.element(key, names(keys))) {
                sig_name <- paste(sig_parts[1:length(sig_parts) - 1],
                                  collapse = "_")
            } else {
                key <- "none"
                sig_name <- sig
            }


            for (k in gene_fields) {
                elem <- strsplit(k, ",")[[1]]

                if (length(elem) > 1) { # if the format is gene,value
                    gene <- elem[1]
                    value <- as.numeric(elem[2])
                } else {
                    gene <- elem[1]
                    value <- keys[key]
                }

                genes <- c(genes, gene)
                values <- c(values, value)
            }

            names(values) <- genes

            if (sig_name %in% names(sig_data)) {
                existingSig <- sig_data[[sig_name]]
                existingSig@sigDict[toupper(names(values))] <- values
                sig_data[[sig_name]] <- existingSig
            } else {
                newSig <- Signature(values, sig_name,
                                    filename, metaData = description)
                sig_data[[sig_name]] <- newSig
            }
        }

    }

    return (sig_data)
}