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To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

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content badge Iframe embedding
swh:1:cnt:2c8edba2b93f83a59bdb528688f8da89ae359474
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

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Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
getIndicesVector <- function(current, neededLength) {
    if (length(current) == 0) {
        current <- 0:(neededLength - 1)
    }
    current + 1
}


#' Reads ExpressionSet from a GCT file.
#'
#' Only versions 1.2 and 1.3 are supported.
#'
#' @param gct Path to gct file
#'
#' @param ... additional options for read.csv
#'
#' @return ExpressionSet object
#'
#' @examples
#' read.gct(system.file("extdata", "centers.gct", package = "phantasus"))
#' @export
read.gct <- function(gct, ...) {
    meta <- readLines(gct, n = 3)
    version <- meta[1]
    size <- as.numeric(unlist(strsplit(meta[2], "\t")))

    if (grepl("^#1.3", version)) {
        # number of column annotations = number of additional rows
        ann.col <- size[4]

        # number of row annotations = number of additional columns
        ann.row <- size[3]
    } else if (grepl("^#1.2", version)) {
        ann.col <- 0
        ann.row <- 1
    } else {
        stop("Unsupported version of gct: use 1.2 or 1.3")
    }

    colNames <- unlist(strsplit(meta[3], "\t"))
    if (grepl("/", colNames[1])) {
        rowIdField <- sub("(.*)/(.*)", "\\1", colNames[1])
        colIdField <- sub("(.*)/(.*)", "\\2", colNames[1])
    } else {
        rowIdField <- "id"
        colIdField <- "id"
    }

    colNames[1] <- rowIdField

    t <- read.tsv(gct, skip = 2 + 1 + ann.col, nrows = size[1],
                col.names = colNames,
                row.names = NULL, header = FALSE,  ...)

    rownames(t) <- t[,1]

    exp <- as.matrix(t[, (ann.row + 2):ncol(t)])

    fdata <- makeAnnotated(t[, seq_len(ann.row), drop = FALSE])


    if (ann.col > 0) {
        pdata.raw <- t(read.tsv(gct, skip = 2, nrows = ann.col,
                                header = FALSE, row.names=NULL))
        pdata <- data.frame(pdata.raw[seq_len(ncol(exp)) + 1 + ann.row, ,
                                drop = FALSE])
        colnames(pdata) <- pdata.raw[1, ]
        colnames(pdata)[1] <- colIdField
        rownames(pdata) <- colnames(exp)
        pdata <- makeAnnotated(pdata)

        res <- ExpressionSet(exp, featureData = fdata, phenoData = pdata)
    } else {
        res <- ExpressionSet(exp, featureData = fdata)
    }

    res
}

read.tsv <- function(file, header = TRUE, sep = "\t", quote = "",
                        comment.char = "",
                        check.names = FALSE, ...) {
    args <- list(...)
    res <- utils::read.table(file, header = header, sep = sep, quote = quote,
                    comment.char = comment.char, check.names = check.names,
                    stringsAsFactors = FALSE,
                    ...)
    if ( (!"row.names" %in% names(args)) && (colnames(res)[1] == "") ) {
        rownames(res) <- res[, 1]
        res[[1]] <- NULL
    }
    res
}

#' Saves ExpressionSet to a GCT file (version 1.3).
#'
#' @param es ExpresionSet obeject to save
#' @param file Path to output gct file
#' @param gzip Whether to gzip apply gzip-compression for the output file#'
#' @param ... additional options for read.csv
#' @return Result of the closing file (as in `close()` function`)
#' @examples
#' es <- read.gct(system.file("extdata", "centers.gct", package = "phantasus"))
#' out <- tempfile(fileext = ".gct.gz")
#' write.gct(es, out, gzip=TRUE)
#' @import Biobase
#' @export
write.gct <- function(es, file, gzip=FALSE) {
    if (gzip) {
        con <- gzfile(file)
    } else {
        con <- file(file)
    }
    open(con, open="w")
    writeLines("#1.3", con)
    ann.col <- ncol(pData(es))
    ann.row <- ncol(fData(es))
    writeLines(sprintf("%s\t%s\t%s\t%s", nrow(es), ncol(es), ann.row, ann.col), con)
    writeLines(paste0(c("ID", colnames(fData(es)), colnames(es)), collapse="\t"), con)

    ann.col.table <- t(as.matrix(pData(es)))
    ann.col.table <- cbind(matrix(rep(NA, ann.row*ann.col), nrow=ann.col), ann.col.table)
    write.table(ann.col.table, file=con, quote=FALSE, sep="\t", row.names=TRUE, col.names=FALSE)
    write.table(cbind(fData(es), exprs(es)), file=con, quote=FALSE, sep="\t", row.names=TRUE, col.names=FALSE)
    close(con)
}


makeAnnotated <- function(data) {
    meta <- data.frame(labelDescription = colnames(data))
    rownames(meta) <- colnames(data)

    methods::new("AnnotatedDataFrame", data = data, varMeta = meta)
}

take <- function(x, n) {
  sapply(x, function(x) {
    x[[n]]
  })
}

writeToList <- function(es) {
  data <- as.matrix(exprs(es))
  colnames(data) <- NULL
  row.names(data) <- NULL

  pdata <- as.matrix(pData(es))
  colnames(pdata) <- NULL
  row.names(pdata) <- NULL

  rownames <- rownames(es)

  fdata <- as.matrix(fData(es))
  colnames(fdata) <- NULL
  row.names(fdata) <- NULL

  res <- list(data = data, pdata = pdata, fdata = fdata,
              rownames = rownames,
              colMetaNames = varLabels(es),
              rowMetaNames = fvarLabels(es))
  res
}

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Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API